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Old 02-07-2014, 02:58 AM   #5
Coryza
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Location: Enschede

Join Date: Feb 2014
Posts: 29
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Reads were generated with Illumina MiSeq 2 paired-end reading. Adapters & Barcodes were trimmed off.

I'm using command bowtie-align -x hg19 -1 [file1] -2 [file2] -S [output] -fr -q

Using extra parameter --local generates 92.50% aligned 0 times.
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