I am puzzled by why a miRNA dataset was sequenced as PE.
Can you check to see if those two reads overlap in the middle (you can use bbmerge.sh from BBMap suite: http://seqanswers.com/forums/showthread.php?t=43906)?
If this is starting to get confusing, just use one of the samples and its *_1.fastq.gz file for initial trial alignment.
Can you check to see if those two reads overlap in the middle (you can use bbmerge.sh from BBMap suite: http://seqanswers.com/forums/showthread.php?t=43906)?
If this is starting to get confusing, just use one of the samples and its *_1.fastq.gz file for initial trial alignment.
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