CLIPSeqTools::PreprocessApp::all - Run all clipseqtools-preprocess analyses.
clipseqtools-preprocess all [options/parameters]
Runs all tools to process a CLIP-Seq FastQ file to a database compatible with clipseqtools. Specifically it will: 1) Trim the adaptor sequence from the end of the reads. 2) Align the reads on a reference genome using STAR aligner. 3) Convert SAM file with alignments into an SQLite database table. 4) Annotate alignments with genic information. 5) Annotate alignments with Repeat Masker. 6) Annotate alignments with deletions. 7) Annotate alignments with conservation.
Input. --fastq <Str> FastQ file with the reads. --adaptor <Str> adaptor sequence. --star_genome <Str> directory with STAR genome index. --rmsk <Str> BED file with repeat masker regions. --gtf <Str> GTF file with genes/transcripts. Output --o_prefix <Str> output path prefix. Script will create and add extension to path. Default: ./ Other input --rname_sizes <Str> file with sizes for reference alignment sequences (rnames). Must be tab delimited (chromosome\tsize) with one line per rname. --cons_dir <Str> directory with phastCons or phyloP files. Other options. --cutadapt_path <Str> path to cutadapt executable. [Default: cutadapt]. --star_path <Str> path to STAR executable. [Default: STAR]. --threads <Int> number of threads to use. [Default: 4]. -v --verbose print progress lines and extra information. -h -? --usage --help print help message
To install CLIPSeqTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CLIPSeqTools
CPAN shell
perl -MCPAN -e shell install CLIPSeqTools
For more information on module installation, please visit the detailed CPAN module installation guide.