NAME

       bam2fastx - tophat component converting bam directly into fastx

DESCRIPTION

   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.

OPTIONS

       -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

bam2fastx 2.1.1+dfsg1-1                           December 2017                                     BAM2FASTX(1)