Samtools flagstat

Question

[michelafrancesconi8]

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

[Pierre Lindenbaum]

Understanding Samtools Flagstat Output ; What Does Samtools Flagstat Results Mean? ; Samtools flagstat results ;

[michelafrancesconi8]

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

[Pierre Lindenbaum]

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

[michelafrancesconi8]

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

[Pierre Lindenbaum]

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

[michelafrancesconi8]

What you suggest me to do?

[aw7]

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

[michelafrancesconi8]

Thank you!