Get the percentage of fragment length that is less than 120bp

Question

[munaj86]

Hi,

I'm working with Cut&Run data and I would like to get the percentage of the fragment length that is less than 120bp. I used bampefragmest size from deep tools to get a plot of all the fragment length that is present in my sample. And now I would like to get the proportion of fragment length that is less than 120bp in the whole sample in order to assess my data.

Can anyone suggest a way to get this, maybe with awk?

Thanks

[ATpoint]

You asked multiple questions but seem to have neither upvoted nor followed up on most of them. Please upvote helpful comments, consider accepting answers that solved the problem.

[munaj86]

I wil do that for the coming question. Thanks

Answer 1

[Alex Reynolds]

You could collect the fragment lengths from the ninth column of the BAM file, and then accumulate them in awk:

$ bam2bed --do-not-sort < reads.bam | awk -v FS="\t" -v THRESHOLD=120 'BEGIN { s = 0; a = 0; } { s += 1; if (($9 < THRESHOLD) && ($9 > -THRESHOLD)) { a += 1 } } END { print a / s; }'

[munaj86]

Hi Alex,

I tried the above command and it gives me 0 with each file. Do you have an idea what might goes wrong?

Thanks