Samtools flagstat
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
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michelafrancesconi8 •
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Thank you, but in your opinion why a have read2 = 0 and all the data in read1? Because no others have it
your bam is paired-end sequencing but all R2 reads are missing.
I see but I don't undersand why and if it's a problem
this is a "problem" with the upstream process that generaed "repressed_C1_tagged_dedup2.bam"
What you suggest me to do?
Ask the person who created the file. Only they will know why the R2 reads are missing in a paired data file.
Thank you!