Question: (Closed) bowtie2 unique align reads
gravatar for Ric
22 months ago by
Ric300 wrote:

I ran bowtie2 in the following way:

bowtie2 -x tdna -U Sample-5-concat+trim-21.fq -S sample5.sam 
1792444 reads; of these:
  1792444 (100.00%) were unpaired; of these:
    1092638 (60.96%) aligned 0 times
    698850 (38.99%) aligned exactly 1 time
    956 (0.05%) aligned >1 times
39.04% overall alignment rate

How do I get reads which aligned exactly 1 time?

Thank you in advance.

alignment • 1.3k views
ADD COMMENTlink written 22 months ago by Ric300

Hello Ric!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink modified 22 months ago • written 22 months ago by ATpoint38k

Thank you it worked.

ADD REPLYlink written 22 months ago by Ric300
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