diff --git a/README.rst b/README.rst index 22a90ef7d93a6fdcbc38d0ffd51eed9cd9ec39c9..287170c3ceb3e659734d12585095d6940d479a8a 100644 --- a/README.rst +++ b/README.rst @@ -39,20 +39,16 @@ Installation List of available tools ----------------------- -*Utility* *Description* +========================= ======================================================================================================= +Utility Description ========================= ======================================================================================================= *intersectBed (BAM)* Returns overlaps between two BED/GFF/VCF files. -*pairToBed (BAM)* Returns overlaps between a paired-end BED file and a - regular BED/VCF/GFF file. -*bamToBed (BAM)* Converts BAM alignments to BED6, BED12, - or BEDPE format. +*pairToBed (BAM)* Returns overlaps between a paired-end BED file and a regular BED/VCF/GFF file. +*bamToBed (BAM)* Converts BAM alignments to BED6, BED12, or BEDPE format. *bedToBam (BAM)* Converts BED/GFF/VCF features to BAM format. -*bed12ToBed6* Converts "blocked" BED12 features to discrete - BED6 features. -*bedToIgv* Creates IGV batch scripts for taking multiple - snapshots from BED/GFF/VCF features. -*coverageBed (BAM)* Summarizes the depth and breadth of coverage of features in one BED versus features - (e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file. +*bed12ToBed6* Converts "blocked" BED12 features to discrete BED6 features. +*bedToIgv* Creates IGV batch scripts for taking multiple snapshots from BED/GFF/VCF features. +*coverageBed (BAM)* Summarizes the depth and breadth of coverage of features in one BED versus features (e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file. *genomeCoverageBed (BAM)* Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage. *unionBedGraphs* Combines multiple BedGraph files into a single file, allowing coverage/other comparisons between them. *annotateBed* Annotates one BED/VCF/GFF file with overlaps from many others.