Copyright 2013 Dmitri Pervouchine (dp@crg.eu), Lab Roderic Guigo Bioinformatics and Genomics Group @ Centre for Genomic Regulation Parc de Recerca Biomedica: Dr. Aiguader, 88, 08003 Barcelona

This file is a part of the 'sjcount' package. 'sjcount' package is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

'sjcount' package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with 'sjcount' package. If not, see http://www.gnu.org/licenses/.

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DESCRIPTION

sjcount is a utility for fast SJ quantification. It is an annotation-agnostic offset-aware vesrion of bam2ssj (see https://github.com/pervouchine/bam2ssj)

This a light version of sjcount-full package (https://github.com/pervouchine/sjcount-full) which does not count multisplits

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INSTALLATION

To install, type 'make all'

Prerequisites: You need samtools, but it will be installed automatically by the makefile Samtools package Version: 0.1.18

NOTE that

1. If samtools is already installed, you can simply update the SAMTOOLS_DIR varibale in the makefile

2. Some users get error messages even when compiling sjcount with a correct SAMDIR path, something like

   /centos6/samtools-9.3.2013/libbam.a(bgzf.o): In function mt_destroy: /centos6/samtools-9.3.2013/bgzf.c:458: undefined reference to pthread_join /centos6/samtools-9.3.2013/libbam.a(bgzf.o): In function bgzf_mt: /centos6/samtools-9.3.2013/bgzf.c:445: undefined reference to pthread_create

This error has to do with big zip libraries, not with samtools.

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USAGE

Usage: ./sjcount -bam bam_file [-ssj junctions_output] [-ssc boundaries_output] [-log log_file] [-read1 0|1] [-read2 0|1] [-nbins number_of_bins] [-lim number_of_lines] [-quiet]

Input: a sorted BAM file with header

Options:

-read1 0/1, reverse complement read1 no/yes (default=1)
-read2 0/1, reverse complement read2 no/yes (default=0)
-nbins number of overhang bins, (default=1)
-maxnh, the max value of the NH tag, (default=none)
-lim nreads stop after nreads, (default=no limit)
-unstranded, force strand to be '.'
-continuous, no mismatches when overlapping splice boundaries
-quiet, suppress verbose output

Output:

-ssj: Splice Junction counts, tab-delimited  (default=stdout)
Columns are: chr, begin, end, strand, offset, count
-ssc: Splice boundary counts, tab-delimited  (default=none)
Columns are: chr, position, strand, offset, count

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DETAILS See documentation in latex/sjcount.pdf