Samtools Flagstat Output Format
I got the following results from running samtools flagstat on single stranded RNA seq data. Can somebody explain what each column means? Did I map incorrectly?
Also, the original fastq file had 4000000 sequences. Is it common to have such a large decrease in sequences?
3267616 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
3267616 + 0 mapped (100.00%:-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)
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Duplicate of What Does Samtools Flagstat Results Mean?
Hello thsay!
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To understand the output of samtools flagstat, Pierre's answer in the linked duplicate post should be what you need.
It looks like the aligner you chose -- or the parameters you used with the aligner -- discarded any reads which did not map to the reference. To say whether or not this outcome is typical is a difficult question to answer without more information about the specific sample type, aligner, aligner parameters, and quality of the FASTQ data.