<commit_before>SYNOPSIS

 RNA-SeqAlign2Ref.pl - The script writes scripts and qsubs to generate
       count summaries for illumina paired or single end reads after mapping against a
       reference genome. The script 1) converts illumina headers if the "-c"
       parameter is used, 2) cleans raw reads using Prinseq
       http://prinseq.sourceforge.net/manual.html, 3) index the reference
       genome for mapping, 4) reads are aligned to the genome with Tophat2
       (read more about Tophat2 at http://tophat.cbcb.umd.edu/manual.html) and
       expressed genes and transcripts are assembled with Cufflinks2, 5) these
       assemblies are merged with Cuffmerge and differential expression is
       estimated with Cuffdiff2.

For examples parameter details run "perl RNA-SeqAlign2Ref.pl -man".

USAGE

        perl RNA-SeqAlign2Ref.pl [options]

        Documentation options:
        -help    brief help message
        -man       full documentation
        Required options:
        -r          filename for file with tab separated list of sample labels, fastq files, and treatment labels
        -f          filename of the reference genome fasta
        -p          project name (no spaces)
        -g          filename of the gtf or gff genome annotation
        Filtering options:
        -l          minimum read length
        Fastq format options:
        -c          convert fastq headers<commit_msg>Update RNA-SeqAlign2RefMANUAL.md<commit_after>SYNOPSIS

 RNA-SeqAlign2Ref.pl - The script writes scripts and qsubs to generate
       count summaries for illumina paired or single end reads after mapping against a
       reference genome. The script 1) converts illumina headers if the "-c"
       parameter is used, 2) cleans raw reads using Prinseq
       http://prinseq.sourceforge.net/manual.html, 3) index the reference
       genome for mapping, 4) reads are aligned to the genome with Tophat2
       (read more about Tophat2 at http://tophat.cbcb.umd.edu/manual.html) and
       expressed genes and transcripts are assembled with Cufflinks2, 5) these
       assemblies are merged with Cuffmerge and differential expression is
       estimated with Cuffdiff2.
       
For examples parameter details run "perl RNA-SeqAlign2Ref.pl -man".
       
UPDATES
       
#####RNA-SeqAlign2Ref.pl Version 1.2 04/17/14

RNA-SeqAlign2Ref.pl  Version 1.2 allows the user to skip read cleaning
(prinseq will only be run to generate read quality metrics without
cleaning) by adding the -n parameter to their script by adding the -n
parameter to their command

#####RNA-SeqAlign2Ref.pl Version 1.1 04/16/14

RNA-SeqAlign2Ref.pl  Version 1.1 - fixed bug in writing index shell
script


USAGE

        perl RNA-SeqAlign2Ref.pl [options]

        Documentation options:
        -help    brief help message
        -man       full documentation
        Required options:
        -r          filename for file with tab separated list of sample labels, fastq files, and treatment labels
        -f          filename of the reference genome fasta
        -p          project name (no spaces)
        -g          filename of the gtf or gff genome annotation
        Filtering options:
        -l          minimum read length
        Fastq format options:
        -c          convert fastq headers
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{'dir': 'git-commits-cleaned', 'id': '528856', 'n_tokens_mistral': 917, 'n_tokens_neox': 836, 'n_words': 381}