Provided by: tophat_2.1.1+dfsg1-1_amd64
bam2fastx - tophat component converting bam directly into fastx
bam2fastx v2.1.1 () usage: bam2fastx [--fasta|-a] [-C|--color] [-P|--paired] [-N] [-A|--all|-M|--mapped-only] [-Q] [--sam|-s|-t] [-o <outfname>] <in.bam> By default, bam2fastx only converts the unmapped reads from the input file, discarding those unmapped reads flagged as QC failed. The input BAM/SAM file MUST be sorted by read name (-n option for samtools sort). If the input file name is "-", stdin will be used instead.
-A,--all convert all reads (mapped and unmapped) (but discarding those flagged as QC failed, unless -Q) -P paired reads are expected and converted into two output files (see <outfname> comments below) -Q convert unmapped reads even when flagged as QC failed -M,--maped-only convert only mapped reads -N for -P, append /1 and /2 suffixes to read names -O ignore the original quality values (OQ tag) and write the current quality values (default is to use OQ data if found) -C,--color reads are in ABI SOLiD color format -s,-t,--sam input is a SAM text file (default: BAM input expected) -a,--fasta output FASTA records, not FASTQ (discard quality values) -o <outfname> output file name or template (see below) <outfname> serves as a name template when -P option is provided, as suffixes .1 and .2 will be automatically inserted before the file extension in <outfname>, such that two file names will be created. If <outfname> ends in .gz or .bz2 then bam2fastx will write the output compressed by gzip or bzip2 respectively. Example of converting all paired reads from a BAM file to FASTQ format: bam2fastx -PANQ -o sample.fq.gz sample.sortedbyname.bam In this example the output will be written in two files: sample.1.fq.gz and sample.2.fq.gz