Question: bowtie2: multi mapping Summary report
0
gravatar for KVC_bioinfo
13 months ago by
KVC_bioinfo320
Boston
KVC_bioinfo320 wrote:

Hello,

I am having a hard time figuring out the summary report from bowtie2.

16182999 reads; of these:
16182999 (100.00%) were paired; of these:
5731231 (35.42%) aligned concordantly 0 times
4522376 (27.95%) aligned concordantly exactly 1 time
5929392 (36.64%) aligned concordantly >1 times
----
5731231 pairs aligned concordantly 0 times; of these:
2381431 (41.55%) aligned discordantly 1 time
----
3349800 pairs aligned 0 times concordantly or discordantly; of these:
6699600 mates make up the pairs; of these:
3814736 (56.94%) aligned 0 times
1883429 (28.11%) aligned exactly 1 time
1001435 (14.95%) aligned >1 times
88.21% overall alignment rate

I am not able to understand which of the above % shows the multi mapping.

Thank you in advance.

bowtie2 • 759 views
ADD COMMENTlink modified 13 months ago by Devon Ryan84k • written 13 months ago by KVC_bioinfo320
1
gravatar for Devon Ryan
13 months ago by
Devon Ryan84k
Freiburg, Germany
Devon Ryan84k wrote:

There are 5929392 paired-end multimappers and 1001435 single-end multimappers. So you can get whatever appropriate percentage you want.

ADD COMMENTlink written 13 months ago by Devon Ryan84k

So it does not mention overall multi mapping?

ADD REPLYlink written 13 months ago by KVC_bioinfo320
1

It makes the most sense to report both numbers ("37% of the paired-end reads and 15% of the remaining singletons were multimapping").

ADD REPLYlink written 13 months ago by Devon Ryan84k
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