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

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

cutandrun
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updated by Ram Ram • written by munaj86 • munaj86

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.

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written by ATpoint ATpoint

I wil do that for the coming question. Thanks

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written by munaj86 • munaj86

1 answer

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; }'
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written by Alex Reynolds Alex Reynolds

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

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written by munaj86 • munaj86

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