Hello all,
I have been given paired-end RNA-Seq files to align against a couple of references. I used Bowtie2 to do the job. The alignment results were very low in most of the cases (less than 5% overall alignment rate).Now, we are thinking this might be caused by either contamination or mix up samples.
Any suggestion what to do in such case?
Thank you in advance
I have been given paired-end RNA-Seq files to align against a couple of references. I used Bowtie2 to do the job. The alignment results were very low in most of the cases (less than 5% overall alignment rate).Now, we are thinking this might be caused by either contamination or mix up samples.
Any suggestion what to do in such case?
Thank you in advance
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