Hi biostars, I have a question about calculating the median read length from a bam file.
samtools view GTEX-1192X-0011-R10a-SM-DO941.bam | awk '{print length($10)}' | head -1000 | sort -u
Instead of the above command line, is it possible to get a median read length from a bam file?
3 answers
samtools view -F 2304 in.bam | awk '{print length($10);}' | datamash median 1
-F 2304 excludes unmapped reads, and datamash is a command line program that makes it easier to perform actions (like column medians) from data in tabular format.
Just remove that argument and run the same command.
-F 2304 excludes unmapped reads
No. It excludes supplementary and secondary reads.
This is what I get for being lazy and thinking I remember what it means instead of looking it up. Thanks for the correction.
Can someone explain the difference between unmapped reads and supplementary reads?
By looking at this discussion, it looks the below command gives the median read lenght of total reads. Can you confirm this, please?
samtools view in.bam | awk '{print length($10);}' | datamash median 1
The referenced command will output ALL reads in the BAM file, because there is no selection being applied. Supplementary reads are described here, and you might be interested in getting familiar with BAM flags by reading the specification or playing with a decoding utility.
If you have littler installed, you could try that:
samtools view mutant_ip.bam | head -1000 | awk '{print length($10)}' | r -de 'print(summary(X[,1]))'
Min. 1st Qu. Median Mean 3rd Qu. Max.
76 76 76 76 76 76
(you would use the median() function in place of summary())
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