\select@language {english}
\contentsline {chapter}{\numberline {1}Table of contents}{3}{chapter.1}
\contentsline {section}{\numberline {1.1}Overview}{3}{section.1.1}
\contentsline {subsection}{\numberline {1.1.1}Background}{3}{subsection.1.1.1}
\contentsline {subsection}{\numberline {1.1.2}Summary of available tools.}{3}{subsection.1.1.2}
\contentsline {subsection}{\numberline {1.1.3}Fundamental concepts.}{4}{subsection.1.1.3}
\contentsline {subsubsection}{What are genome features and how are they represented?}{4}{subsubsection*.3}
\contentsline {subsubsection}{Overlapping / intersecting features.}{5}{subsubsection*.4}
\contentsline {subsubsection}{Comparing features in file \IeC {\textquotedblleft }A\IeC {\textquotedblright } and file \IeC {\textquotedblleft }B\IeC {\textquotedblright }.}{5}{subsubsection*.5}
\contentsline {subsubsection}{BED starts are zero-based and BED ends are one-based.}{5}{subsubsection*.6}
\contentsline {subsubsection}{GFF starts and ends are one-based.}{5}{subsubsection*.7}
\contentsline {subsubsection}{VCF coordinates are one-based.}{6}{subsubsection*.8}
\contentsline {subsubsection}{File B is loaded into memory (most of the time).}{6}{subsubsection*.9}
\contentsline {subsubsection}{Feature files \emph {must} be tab-delimited.}{6}{subsubsection*.10}
\contentsline {subsubsection}{All bedtools allow features to be \IeC {\textquotedblleft }piped\IeC {\textquotedblright } via standard input.}{6}{subsubsection*.11}
\contentsline {subsubsection}{Most bedtools write their results to standard output.}{6}{subsubsection*.12}
\contentsline {subsubsection}{What is a \IeC {\textquotedblleft }genome\IeC {\textquotedblright } file?}{7}{subsubsection*.13}
\contentsline {subsubsection}{Paired-end BED files (BEDPE files).}{7}{subsubsection*.14}
\contentsline {subsubsection}{Use \IeC {\textquotedblleft }-h\IeC {\textquotedblright } for help with any bedtool.}{7}{subsubsection*.15}
\contentsline {subsubsection}{BED features must not contain negative positions.}{7}{subsubsection*.16}
\contentsline {subsubsection}{The start position must be \textless {}= to the end position.}{7}{subsubsection*.17}
\contentsline {subsubsection}{Headers are allowed in GFF and BED files}{7}{subsubsection*.18}
\contentsline {subsubsection}{GZIP support: BED, GFF, VCF, and BEDPE file can be \IeC {\textquotedblleft }gzipped\IeC {\textquotedblright }}{8}{subsubsection*.19}
\contentsline {subsubsection}{Support for \IeC {\textquotedblleft }split\IeC {\textquotedblright } or \IeC {\textquotedblleft }spliced\IeC {\textquotedblright } BAM alignments and \IeC {\textquotedblleft }blocked\IeC {\textquotedblright } BED features}{8}{subsubsection*.20}
\contentsline {subsubsection}{Writing uncompressed BAM output.}{8}{subsubsection*.21}
\contentsline {subsection}{\numberline {1.1.4}Implementation and algorithmic notes.}{8}{subsection.1.1.4}
\contentsline {section}{\numberline {1.2}Installation}{9}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}Installing stable releases}{9}{subsection.1.2.1}
\contentsline {subsubsection}{Compiling from source via Google Code}{9}{subsubsection*.22}
\contentsline {subsubsection}{Installing with package managers}{9}{subsubsection*.23}
\contentsline {subsection}{\numberline {1.2.2}Development versions}{10}{subsection.1.2.2}
\contentsline {section}{\numberline {1.3}Quick start}{10}{section.1.3}
\contentsline {subsection}{\numberline {1.3.1}Install bedtools}{10}{subsection.1.3.1}
\contentsline {subsection}{\numberline {1.3.2}Use bedtools}{10}{subsection.1.3.2}
\contentsline {section}{\numberline {1.4}General usage}{11}{section.1.4}
\contentsline {subsection}{\numberline {1.4.1}Supported file formats}{11}{subsection.1.4.1}
\contentsline {subsubsection}{BED format}{11}{subsubsection*.24}
\contentsline {subsubsection}{BEDPE format}{13}{subsubsection*.25}
\contentsline {subsubsection}{GFF format}{14}{subsubsection*.26}
\contentsline {subsubsection}{\emph {Genome} file format}{15}{subsubsection*.27}
\contentsline {subsubsection}{SAM/BAM format}{15}{subsubsection*.28}
\contentsline {subsubsection}{VCF format}{16}{subsubsection*.29}
\contentsline {section}{\numberline {1.5}The BEDTools suite}{16}{section.1.5}
\contentsline {subsection}{\numberline {1.5.1}The full list of \emph {bedtools} sub-commands.}{16}{subsection.1.5.1}
\contentsline {subsubsection}{\emph {annotate}}{16}{subsubsection*.30}
\contentsline {paragraph}{Usage and option summary}{16}{paragraph*.31}
\contentsline {paragraph}{Default behavior - annotate one file with coverage from others.}{17}{paragraph*.32}
\contentsline {paragraph}{\texttt {-count} Report the count of hits from the annotation files}{17}{paragraph*.33}
\contentsline {paragraph}{\texttt {-both} Report both the count of hits and the fraction covered from the annotation files}{18}{paragraph*.34}
\contentsline {paragraph}{\texttt {-s} Restrict the reporting to overlaps on the \textbf {same} strand.}{18}{paragraph*.35}
\contentsline {paragraph}{\texttt {-S} Restrict the reporting to overlaps on the \textbf {opposite} strand.}{18}{paragraph*.36}
\contentsline {subsubsection}{\emph {bamtobed}}{18}{subsubsection*.37}
\contentsline {paragraph}{Usage and option summary}{18}{paragraph*.38}
\contentsline {paragraph}{Default behavior}{19}{paragraph*.39}
\contentsline {paragraph}{\texttt {-tag} Set the score field based on BAM tags}{19}{paragraph*.40}
\contentsline {paragraph}{\texttt {-bedpe} Set the score field based on BAM tags}{20}{paragraph*.41}
\contentsline {paragraph}{\texttt {-split} Creating BED12 features from ``spliced'' BAM entries.}{20}{paragraph*.42}
\contentsline {subsubsection}{\emph {bamtofastq}}{20}{subsubsection*.43}
\contentsline {paragraph}{Usage and option summary}{21}{paragraph*.44}
\contentsline {paragraph}{Default behavior}{21}{paragraph*.45}
\contentsline {paragraph}{\texttt {-fq2} Creating two FASTQ files for paired-end sequences.}{21}{paragraph*.46}
\contentsline {subsubsection}{\emph {bed12tobed6}}{22}{subsubsection*.47}
\contentsline {paragraph}{Usage and option summary}{22}{paragraph*.48}
\contentsline {paragraph}{Default behavior}{22}{paragraph*.49}
\contentsline {subsubsection}{\emph {bedpetobam}}{23}{subsubsection*.50}
\contentsline {subsubsection}{\emph {bedtobam}}{23}{subsubsection*.51}
\contentsline {paragraph}{Usage and option summary}{23}{paragraph*.52}
\contentsline {paragraph}{Default behavior}{23}{paragraph*.53}
\contentsline {paragraph}{Creating ``spliced'' BAM entries from ``blocked'' BED features}{23}{paragraph*.54}
\contentsline {subsubsection}{\emph {closest}}{24}{subsubsection*.55}
\contentsline {paragraph}{5.6.1 Usage and option summary}{24}{paragraph*.56}
\contentsline {paragraph}{Default behavior}{24}{paragraph*.57}
\contentsline {paragraph}{\texttt {-s} Enforcing ``strandedness''}{25}{paragraph*.58}
\contentsline {paragraph}{\texttt {-t} Controlling how ties for ``closest'' are broken}{25}{paragraph*.59}
\contentsline {paragraph}{\texttt {-d} Reporting the distance to the closest feature in base pairs}{26}{paragraph*.60}
\contentsline {subsubsection}{\emph {cluster}}{26}{subsubsection*.61}
\contentsline {paragraph}{Usage and option summary}{27}{paragraph*.62}
\contentsline {paragraph}{Default behavior}{27}{paragraph*.63}
\contentsline {paragraph}{\texttt {-s} Enforcing ``strandedness''}{27}{paragraph*.64}
\contentsline {paragraph}{\texttt {-d} Controlling how close two features must be in order to cluster}{28}{paragraph*.65}
\contentsline {subsubsection}{\emph {complement}}{28}{subsubsection*.66}
\contentsline {paragraph}{Usage and option summary}{29}{paragraph*.67}
\contentsline {paragraph}{Default behavior}{29}{paragraph*.68}
\contentsline {subsubsection}{\emph {coverage}}{29}{subsubsection*.69}
\contentsline {paragraph}{Usage and option summary}{29}{paragraph*.70}
\contentsline {paragraph}{Default behavior}{30}{paragraph*.71}
\contentsline {paragraph}{\texttt {-s} Calculating coverage by strand}{31}{paragraph*.72}
\contentsline {paragraph}{\texttt {-hist} Creating a histogram of coverage for each feature in the B file}{31}{paragraph*.73}
\contentsline {paragraph}{\texttt {-hist} Reporting the per-base of coverage for each feature in the B file}{32}{paragraph*.74}
\contentsline {paragraph}{\texttt {-split} Reporting coverage with spliced alignments or blocked BED features}{32}{paragraph*.75}
\contentsline {subsubsection}{\emph {expand}}{33}{subsubsection*.76}
\contentsline {subsubsection}{\emph {flank}}{33}{subsubsection*.77}
\contentsline {subsubsection}{\emph {genomecov}}{33}{subsubsection*.78}
\contentsline {paragraph}{Usage and option summary}{33}{paragraph*.79}
\contentsline {paragraph}{Default behavior}{34}{paragraph*.80}
\contentsline {paragraph}{\texttt {-max} Controlling the histogram's maximum depth}{34}{paragraph*.81}
\contentsline {paragraph}{\texttt {-d} Reporting ``per-base'' genome coverage}{34}{paragraph*.82}
\contentsline {paragraph}{\texttt {-split} Reporting coverage with spliced alignments or blocked BED features}{35}{paragraph*.83}
\contentsline {subsubsection}{\emph {getfasta}}{35}{subsubsection*.84}
\contentsline {paragraph}{Usage and option summary}{35}{paragraph*.85}
\contentsline {paragraph}{Default behavior}{36}{paragraph*.86}
\contentsline {paragraph}{\texttt {-name} Using the BED ``name'' column as a FASTA header.}{36}{paragraph*.87}
\contentsline {paragraph}{\texttt {-tab} Creating a tab-delimited output file in lieu of FASTA output.}{37}{paragraph*.88}
\contentsline {paragraph}{\texttt {-s} Forcing the extracted sequence to reflect the requested strand}{37}{paragraph*.89}
\contentsline {paragraph}{\texttt {-split} Extracting BED ``blocks''.}{37}{paragraph*.90}
\contentsline {subsubsection}{\emph {groupby}}{39}{subsubsection*.91}
\contentsline {paragraph}{Usage and option summary}{39}{paragraph*.92}
\contentsline {paragraph}{Default behavior.}{40}{paragraph*.93}
\contentsline {paragraph}{Computing the min and max.}{41}{paragraph*.94}
\contentsline {paragraph}{Computing the mean and median.}{41}{paragraph*.95}
\contentsline {paragraph}{Computing the mode and ``antimode''.}{42}{paragraph*.96}
\contentsline {paragraph}{Computing the count of lines for a given group.}{42}{paragraph*.97}
\contentsline {paragraph}{Collapsing: listing all of the values in the opCol for a given group.}{42}{paragraph*.98}
\contentsline {paragraph}{Computing frequencies: freqasc and freqdesc.}{42}{paragraph*.99}
\contentsline {subsubsection}{\emph {intersect}}{43}{subsubsection*.100}
\contentsline {paragraph}{Usage and option summary}{44}{paragraph*.101}
\contentsline {paragraph}{Default behavior}{44}{paragraph*.102}
\contentsline {paragraph}{\texttt {-wa} Reporting the original A feature}{45}{paragraph*.103}
\contentsline {paragraph}{\texttt {-wb} Reporting the original B feature}{45}{paragraph*.104}
\contentsline {paragraph}{\texttt {-loj} Left outer join. Report features in A with and without overlaps}{46}{paragraph*.105}
\contentsline {paragraph}{\texttt {-wo} Write the \emph {amount} of overlap between intersecting features}{46}{paragraph*.106}
\contentsline {paragraph}{\texttt {-wao} Write \emph {amounts} of overlap for all features.}{47}{paragraph*.107}
\contentsline {paragraph}{\texttt {-u} (unique) Reporting the mere presence of \emph {any} overlapping features}{47}{paragraph*.108}
\contentsline {paragraph}{\texttt {-c} Reporting the number of overlapping features}{47}{paragraph*.109}
\contentsline {paragraph}{\texttt {-v} Reporting the absence of any overlapping features}{48}{paragraph*.110}
\contentsline {paragraph}{\texttt {-f} Requiring a minimal overlap fraction}{48}{paragraph*.111}
\contentsline {paragraph}{\texttt {-r, and -f} Requiring reciprocal minimal overlap fraction}{48}{paragraph*.112}
\contentsline {paragraph}{\texttt {-s} Enforcing \emph {same} strandedness}{49}{paragraph*.113}
\contentsline {paragraph}{\texttt {-S} Enforcing \emph {opposite} ``strandedness''}{49}{paragraph*.114}
\contentsline {paragraph}{\texttt {-abam} Default behavior when using BAM input}{49}{paragraph*.115}
\contentsline {paragraph}{\texttt {-ubam} Default behavior when using BAM input}{50}{paragraph*.116}
\contentsline {paragraph}{\texttt {-bed} Output BED format when using BAM input}{50}{paragraph*.117}
\contentsline {paragraph}{\texttt {-split} Reporting overlaps with spliced alignments or blocked BED features}{51}{paragraph*.118}
\contentsline {paragraph}{\texttt {-sorted} Invoke a memory-efficient algorithm for very large files.}{51}{paragraph*.119}
\contentsline {paragraph}{\texttt {-header} Print the header for the A file before reporting results.}{51}{paragraph*.120}
\contentsline {subsubsection}{\emph {jaccard}}{52}{subsubsection*.121}
\contentsline {subsubsection}{\emph {links}}{52}{subsubsection*.122}
\contentsline {paragraph}{Usage and option summary}{52}{paragraph*.123}
\contentsline {paragraph}{Default behavior}{52}{paragraph*.124}
\contentsline {paragraph}{Creating HTML links to a local UCSC Browser installation}{52}{paragraph*.125}
\contentsline {subsubsection}{\emph {makewindows}}{53}{subsubsection*.126}
\contentsline {subsubsection}{\emph {map}}{53}{subsubsection*.127}
\contentsline {paragraph}{Usage and option summary}{54}{paragraph*.128}
\contentsline {paragraph}{Default behavior - compute the \texttt {sum} of the \texttt {score} column for all overlaps.}{56}{paragraph*.129}
\contentsline {paragraph}{\texttt {mean} Compute the mean of a column from overlapping intervals}{56}{paragraph*.130}
\contentsline {paragraph}{\texttt {collapse} List each value of a column from overlapping intervals}{56}{paragraph*.131}
\contentsline {paragraph}{\texttt {distinct} List each \emph {unique} value of a column from overlapping intervals}{57}{paragraph*.132}
\contentsline {paragraph}{\texttt {-s} Only include intervals that overlap on the \emph {same} strand.}{57}{paragraph*.133}
\contentsline {paragraph}{\texttt {-S} Only include intervals that overlap on the \emph {opposite} strand.}{57}{paragraph*.134}
\contentsline {subsubsection}{\emph {maskfasta}}{57}{subsubsection*.135}
\contentsline {paragraph}{Usage and option summary}{57}{paragraph*.136}
\contentsline {paragraph}{Default behavior}{58}{paragraph*.137}
\contentsline {paragraph}{\texttt {-soft} Soft-masking the FASTA file.}{58}{paragraph*.138}
\contentsline {paragraph}{\texttt {-mc} Specify a masking character.}{59}{paragraph*.139}
\contentsline {subsubsection}{\emph {merge}}{59}{subsubsection*.140}
\contentsline {paragraph}{Usage and option summary}{60}{paragraph*.141}
\contentsline {paragraph}{Default behavior}{60}{paragraph*.142}
\contentsline {paragraph}{\texttt {-s} Enforcing ``strandedness''}{60}{paragraph*.143}
\contentsline {paragraph}{\texttt {-n} Reporting the number of features that were merged}{61}{paragraph*.144}
\contentsline {paragraph}{\texttt {-d} Controlling how close two features must be in order to merge}{61}{paragraph*.145}
\contentsline {paragraph}{\texttt {-nms} Reporting the names of the features that were merged}{61}{paragraph*.146}
\contentsline {paragraph}{\texttt {-scores} Reporting the scores of the features that were merged}{62}{paragraph*.147}
\contentsline {subsubsection}{\emph {multicov}}{62}{subsubsection*.148}
\contentsline {paragraph}{Usage and option summary}{62}{paragraph*.149}
\contentsline {paragraph}{Default behavior.}{63}{paragraph*.150}
\contentsline {subsubsection}{\emph {multiinter}}{64}{subsubsection*.151}
\contentsline {subsubsection}{\emph {nuc}}{64}{subsubsection*.152}
\contentsline {subsubsection}{\emph {overlap}}{64}{subsubsection*.153}
\contentsline {paragraph}{Usage and option summary}{64}{paragraph*.154}
\contentsline {paragraph}{Default behavior}{64}{paragraph*.155}
\contentsline {subsubsection}{\emph {pairtobed}}{64}{subsubsection*.156}
\contentsline {subsubsection}{\emph {pairtopair}}{64}{subsubsection*.157}
\contentsline {paragraph}{Usage and option summary}{64}{paragraph*.158}
\contentsline {paragraph}{Default behavior}{65}{paragraph*.159}
\contentsline {paragraph}{\texttt {-type neither} Optional overlap requirements}{66}{paragraph*.160}
\contentsline {subsubsection}{\emph {random}}{66}{subsubsection*.161}
\contentsline {paragraph}{Usage and option summary}{67}{paragraph*.162}
\contentsline {paragraph}{Default behavior}{68}{paragraph*.163}
\contentsline {paragraph}{\texttt {-n} Specify the \emph {number} of intervals to generate.}{68}{paragraph*.164}
\contentsline {paragraph}{\texttt {-l} Specify the \emph {length} of intervals to generate.}{69}{paragraph*.165}
\contentsline {paragraph}{\texttt {-seed} Defining a ``seed'' for the random interval creation.}{69}{paragraph*.166}
\contentsline {subsubsection}{\emph {shuffle}}{69}{subsubsection*.167}
\contentsline {paragraph}{Usage and option summary}{70}{paragraph*.168}
\contentsline {paragraph}{Default behavior}{71}{paragraph*.169}
\contentsline {paragraph}{\texttt {-chrom} Requiring that features be shuffled on the same chromosome}{71}{paragraph*.170}
\contentsline {paragraph}{\texttt {-excl} Excluding certain genome regions from \texttt {bedtools shuffle}}{72}{paragraph*.171}
\contentsline {paragraph}{\texttt {-seed} Defining a ``seed'' for the random replacement.}{72}{paragraph*.172}
\contentsline {subsubsection}{\emph {slop}}{73}{subsubsection*.173}
\contentsline {paragraph}{Usage and option summary}{74}{paragraph*.174}
\contentsline {paragraph}{Default behavior}{74}{paragraph*.175}
\contentsline {paragraph}{\texttt {-s} Resizing features according to strand}{75}{paragraph*.176}
\contentsline {paragraph}{\texttt {-pct} Resizing features by a given fraction}{75}{paragraph*.177}
\contentsline {paragraph}{\texttt {-header} Print the header for the A file before reporting results.}{75}{paragraph*.178}
\contentsline {subsubsection}{\emph {sort}}{75}{subsubsection*.179}
\contentsline {paragraph}{Usage and option summary}{76}{paragraph*.180}
\contentsline {paragraph}{Default behavior}{76}{paragraph*.181}
\contentsline {paragraph}{Optional sorting behavior}{76}{paragraph*.182}
\contentsline {subsubsection}{\emph {subtract}}{77}{subsubsection*.183}
\contentsline {paragraph}{Usage and option summary}{77}{paragraph*.184}
\contentsline {paragraph}{Default behavior}{78}{paragraph*.185}
\contentsline {paragraph}{\texttt {-f} Requiring a minimal overlap fraction before subtracting}{78}{paragraph*.186}
\contentsline {paragraph}{\texttt {-s} Enforcing same ``strandedness''}{78}{paragraph*.187}
\contentsline {paragraph}{\texttt {-S} Enforcing opposite ``strandedness''}{79}{paragraph*.188}
\contentsline {paragraph}{\texttt {-A} Remove features with any overlap}{79}{paragraph*.189}
\contentsline {subsubsection}{\emph {tag}}{79}{subsubsection*.190}
\contentsline {subsubsection}{\emph {unionbedg}}{79}{subsubsection*.191}
\contentsline {paragraph}{Usage and option summary}{79}{paragraph*.192}
\contentsline {paragraph}{Default behavior}{80}{paragraph*.193}
\contentsline {paragraph}{\texttt {-header} Add a header line to the output}{80}{paragraph*.194}
\contentsline {paragraph}{\texttt {-names} Add a header line with custom file names to the output}{81}{paragraph*.195}
\contentsline {paragraph}{\texttt {-empty} Include regions that have zero coverage in all BEDGRAPH files.}{81}{paragraph*.196}
\contentsline {paragraph}{\texttt {-filler} Use a custom value for missing values.}{81}{paragraph*.197}
\contentsline {paragraph}{Use BEDGRAPH files with non-numeric values.}{82}{paragraph*.198}
\contentsline {subsubsection}{\emph {window}}{82}{subsubsection*.199}
\contentsline {paragraph}{Usage and option summary}{83}{paragraph*.200}
\contentsline {paragraph}{Default behavior}{84}{paragraph*.201}
\contentsline {paragraph}{\texttt {-w} Defining a custom window size}{84}{paragraph*.202}
\contentsline {paragraph}{\texttt {-l and -r} Defining \emph {assymteric} windows}{85}{paragraph*.203}
\contentsline {paragraph}{\texttt {-sw} Defining assymteric windows based on strand}{85}{paragraph*.204}
\contentsline {paragraph}{\texttt {-sm} Enforcing matches with the \emph {same} ``strandedness''}{86}{paragraph*.205}
\contentsline {paragraph}{\texttt {-Sm} Enforcing matches with the \emph {same} ``strandedness''}{86}{paragraph*.206}
\contentsline {paragraph}{\texttt {-u} Reporting the presence/absence of at least one overlapping feature}{86}{paragraph*.207}
\contentsline {paragraph}{\texttt {-c} Reporting the number of overlapping features}{86}{paragraph*.208}
\contentsline {paragraph}{\texttt {-v} Reporting the absence of any overlapping features}{86}{paragraph*.209}
\contentsline {paragraph}{\texttt {-header} Print the header for the A file before reporting results.}{86}{paragraph*.210}
\contentsline {section}{\numberline {1.6}Example usage}{86}{section.1.6}
\contentsline {subsection}{\numberline {1.6.1}bedtools intersect}{87}{subsection.1.6.1}
\contentsline {subsection}{\numberline {1.6.2}bedtools bamtobed}{87}{subsection.1.6.2}
\contentsline {subsection}{\numberline {1.6.3}bedtools window}{88}{subsection.1.6.3}
\contentsline {subsection}{\numberline {1.6.4}bedtools closest}{88}{subsection.1.6.4}
\contentsline {subsection}{\numberline {1.6.5}bedtools subtract}{88}{subsection.1.6.5}
\contentsline {subsection}{\numberline {1.6.6}bedtools merge}{88}{subsection.1.6.6}
\contentsline {subsection}{\numberline {1.6.7}bedtools coverage}{89}{subsection.1.6.7}
\contentsline {subsection}{\numberline {1.6.8}bedtools complement}{89}{subsection.1.6.8}
\contentsline {subsection}{\numberline {1.6.9}bedtools shuffle}{89}{subsection.1.6.9}
\contentsline {section}{\numberline {1.7}Advanced usage}{90}{section.1.7}
\contentsline {subsection}{\numberline {1.7.1}Mask all regions in a genome except for targeted capture regions.}{90}{subsection.1.7.1}
\contentsline {subsection}{\numberline {1.7.2}Screening for novel SNPs.}{90}{subsection.1.7.2}
\contentsline {subsection}{\numberline {1.7.3}Computing the coverage of features that align entirely within an interval.}{90}{subsection.1.7.3}
\contentsline {subsection}{\numberline {1.7.4}Computing the coverage of BAM alignments on exons.}{90}{subsection.1.7.4}
\contentsline {subsection}{\numberline {1.7.5}Computing coverage separately for each strand.}{90}{subsection.1.7.5}
\contentsline {section}{\numberline {1.8}Tips and Tricks}{91}{section.1.8}
\contentsline {subsection}{\numberline {1.8.1}The \texttt {-sorted} option}{91}{subsection.1.8.1}
\contentsline {section}{\numberline {1.9}FAQ}{91}{section.1.9}
\contentsline {subsection}{\numberline {1.9.1}Installation issues}{91}{subsection.1.9.1}
\contentsline {subsubsection}{Why am I getting all of these zlib errors?}{91}{subsubsection*.211}
\contentsline {subsection}{\numberline {1.9.2}General questions}{91}{subsection.1.9.2}
\contentsline {subsubsection}{How do I know what version of bedtools I am using?}{91}{subsubsection*.212}
\contentsline {subsubsection}{How do I bring up the help/usage menu?}{92}{subsubsection*.213}
\contentsline {section}{\numberline {1.10}Related software}{92}{section.1.10}
\contentsline {subsection}{\numberline {1.10.1}IGV}{92}{subsection.1.10.1}
\contentsline {subsection}{\numberline {1.10.2}Galaxy}{93}{subsection.1.10.2}
\contentsline {subsection}{\numberline {1.10.3}Pybedtools}{94}{subsection.1.10.3}
\contentsline {subsection}{\numberline {1.10.4}MISO}{94}{subsection.1.10.4}
\contentsline {subsection}{\numberline {1.10.5}RetroSeq}{94}{subsection.1.10.5}
\contentsline {chapter}{\numberline {2}Brief example}{95}{chapter.2}
\contentsline {chapter}{\numberline {3}License}{97}{chapter.3}
\contentsline {chapter}{\numberline {4}Acknowledgments}{99}{chapter.4}
\contentsline {chapter}{\numberline {5}Mailing list}{101}{chapter.5}
