Bam2fastx converts bam directly into fastx. 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 flagsUse the -O option to ignore the OQ tag, if present, when writing quality values
Parent program: tophat
TopHat is a fast tool for splice junction mapping for RNA-Seq reads. It aligns reads to genome using the high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. It can work without a reference annotation and process mammalian-sized genomes.