Samtools flagstat
0
0
Entering edit mode
11 weeks ago

Hi, i don't undersand if my data are good and how interprete it

samtools flagstat repressed_C1_tagged_dedup2.bam

3318824 + 14722 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
3318824 + 11471 mapped (100.00% : 77.92%)
3288632 + 14722 paired in sequencing
3288632 + 14722 read1
0 + 0 read2
3269034 + 7714 properly paired (99.40% : 52.40%)
3288632 + 11471 with itself and mate mapped
0 + 0 singletons (0.00% : 0.00%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Can someone help me? Thanks

Samtools • 497 views
ADD COMMENT
0
Entering edit mode

Thank you, but in your opinion why a have read2 = 0 and all the data in read1? Because no others have it

ADD REPLY
0
Entering edit mode

your bam is paired-end sequencing but all R2 reads are missing.

ADD REPLY
0
Entering edit mode

I see but I don't undersand why and if it's a problem

ADD REPLY
0
Entering edit mode

this is a "problem" with the upstream process that generaed "repressed_C1_tagged_dedup2.bam"

ADD REPLY
0
Entering edit mode

What you suggest me to do?

ADD REPLY
0
Entering edit mode

Ask the person who created the file. Only they will know why the R2 reads are missing in a paired data file.

ADD REPLY
0
Entering edit mode

Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 788 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6