NAME¶

bam2fastx - tophat component converting bam directly into fastx

SYNOPSIS¶

bam2fastx [ --fasta|-a|--fastq|-q] [--color] [-Q] [--sam|-s|-t]

DESCRIPTION¶

[-M|--mapped-only|-A|--all] [-o <outfile>] [-P|--paired] [-N] <in.bam>

Note: By default, reads flagged as not passing quality controls are

discarded; the -Q option can be used to ignore the QC flag.

Use the -N option if the /1 and /2 suffixes should be appended to

read names according to the SAM flags

Use the -O option to ignore the OQ tag, if present, when writing quality values