Question: (Closed) Samtools Flagstat Output Format
gravatar for thsay
5.3 years ago by
United States
thsay0 wrote:

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)
rna-seq samtools • 4.7k views
ADD COMMENTlink written 5.3 years ago by thsay0

duplicate of What Does Samtools Flagstat Results Mean?

ADD REPLYlink written 5.3 years ago by Pierre Lindenbaum131k

Hello thsay!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 5.3 years ago by Dan D7.1k

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.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Dan D7.1k
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