Hello,
I have troubles extracting the best score peaks from my bed file.
I have something like this :
chr1 4483445 4484123 MACS_peak_1 59.19
chr1 4533929 4534670 MACS_peak_2 291.66
chr1 4561472 4562345 MACS_peak_3 492.41
chr1 4661528 4662199 MACS_peak_4 72.40
chr1 4695864 4697136 MACS_peak_5 204.10
chr1 4745953 4746562 MACS_peak_6 420.59
and I would like to extract just the peaks that are above a threshold for the score (ex : 100) (5th column)
I have tried with bedtools, but it can just sort them by chromosome then score, and I don't find how to extract just the lines with a score above 100.
I succeed to extract them with unix using sort then tail, but afterward, when I write the output, and try to work with the file, I have an issue since unix don't write the 5th column as integer but as numerical.
Is there anyhow a better way to do it ?
Thank you
•
written
by
giroudpaul
Well, this just worked, thank you for the ultra quick answer.
I wanted to restrain my bed file before putting it into GREAT, and I told me it won't accept it because 5th column was not an interger, so that's were I didn't understood.
Anyway, thank you
Edit : actually, it still don't work with GREAT...
Error details:
Line X: The fifth field (score) must be an integer (not 291.66). Input data: 'chr1 4533929 4534670 MACS_peak_2 291.66'
Then you'll need to round:
awk 'BEGIN{OFS="\t"}{if($5>100) {$5 = int($5); print $0}}' input.bed > output.bed
This always rounds down, but you could do things differently if needed.
This work just fine, thank you !
awk '{if($5>100) print $0}' input.bed > output.bed
The fifth column isn't an interger, so I'm not sure why you're surprised that it's not automagically being made into one.
For brevity, you can also do:
$ awk '$5 > 100' input.bed > output.bed
Log in to answer this question.