I would like to further examine reads that Tophat didn't manage to align in a first run and i wonder, if there is any easy way to get these reads. With Bowtie this would be easy using the "--un" argument, but Tophat doesn't seem to have smth like this. I am so far able to extract read-ids of the reads that do align by:
From that point i'd need to extract fastq-entries that don't match any of the lines in the readIds file. Since FastQ-entries do not consist of single lines i got stuck here - any ideas/help would be appreciated!
Thanks in advance & Cheers
Uwe
Code:
cut --fields=1 accepted_hits.sam | sort --unique > accepted_hits_readsIds.txt
Thanks in advance & Cheers
Uwe
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