Filtering uniuque reads from a bam file
Hello everyone,
I created a bam file with tophat:
I thought with using the -x 1 option to remove all reads which were mapped multiple times. But when looking in IGV, only the reads mapping in different transcripts at exactly the same place were removed (now I found this thread, where this was discussed). With the -G option I only discard the reads which where mapped multiple times, but still keeping 1 read. I want to remove them all when they are not unique.
How can I do this?
Is there another option in tophat which can do this for me?
Is there a tool which can do this for me?
Or do I have to write a script to remove all reads with the same name as the reads with a HI tag of 1 or higher?
I created a bam file with tophat:
Code:
tophat2 --color --quals -x 1 --library-type fr-secondstrand --read-realign-edit-dist 0 -N 10 -m 2 --read-edit-dist 10 --coverage-search --bowtie1 -o {outdir} {genomeIndex} {F3.csfasta} {F5.csfasta} {F3.qual} {F5.qual}
How can I do this?
Is there another option in tophat which can do this for me?
Is there a tool which can do this for me?
Or do I have to write a script to remove all reads with the same name as the reads with a HI tag of 1 or higher?