I wanted to ask about
accepted_hits.bam file from TopHat. Is it correct that it does not contain all the valid alignments?
If it is true then I can conclude that the input fasta file should have some alignments which are not include in this file (maybe the ones which their associated reads are not unique are excluded(?) ). So, if I need all the alignments of my fasta file not only the ones in accepted_hits.bam file should I merge any TopHat output files?
Any suggestion would be appreciated.