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Question: How can I see the amount of reads and aligned reads from Bowtie?
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gravatar for dchalagarcia
22 months ago by
dchalagarcia • 0
dchalagarcia • 0 wrote:

Hi,

I am trying to see the amount of reads produced by Bowtie and also the number of aligned reads. I chose the stats option before running Bowtie. It gave me the stats for one of the runs (on defult settings) but it did not give me the stats for the second run (on Very sensitive).

Does anyone know how else to see these stats?

Thank you
bowtie • 880 views
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modified 22 months ago by Bao Ho • 80 • written 22 months ago by dchalagarcia • 0
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gravatar for Bao Ho
22 months ago by
Bao Ho • 80
UCSF
Bao Ho • 80 wrote:

You can use Flagstat on your alignment results (SAM/BAM).

This is an example of the text file result that I get from Flagstat:

30407764 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 secondary

0 + 0 duplicates

19468353 + 0 mapped (64.02%:-nan%)

0 + 0 paired in sequencing

0 + 0 read1

0 + 0 read2

0 + 0 properly paired (-nan%:-nan%)

0 + 0 with itself and mate mapped

0 + 0 singletons (-nan%:-nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)
ADD COMMENT • link modified 22 months ago • written 22 months ago by Bao Ho • 80

This is great, thank you!

ADD REPLY • link written 22 months ago by dchalagarcia • 0
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