How to see maximal read length / average read length using STAR

Question

[shinyjj]

I am trying to understand the length of the short reads in star.png. In the screenshot, the average is 90, but as I know that’s not how this is defined for illumina. If the average is 90 mapped, the actual length is ~100 with the rest going to adapters. Is there a way to see the maximal length of a read (e.g. something like check the max length of the first 5k of the reads)?

Answer 1

[Istvan Albert]

You can run a tool like seqkit stats, or run for a quick solution run something like:

cat data.fq | awk 'NR%4==2 { print length($0) }' | datamash mean 1 median 1