Hello, I'm having a problem with bedtools that I don't know how to solve. I have a file with this kind of information:
chr19 frame_2_peak_20020 noCDS 184940 185402 . + . 433
And another one with:
chr19 StrAnA transcript 184909 186112 . + . gene_id "candidate_350";
They are obviously overlapping, however when I do:
bedtools coverage -a candidates_noint.sorted.gtf -b peaks_78.sorted.gtf -s
I get the following result:
chr19 StrAnA transcript 184909 186112 . + . gene_id "candidate_350"; 0 0 1204 0.0000000
I don't get why I'm getting this result, I checked the format like 100 times, maybe I'm not seeing something :/
I tried to use bedtools intersect and as expected after see the results I got with coverage I get an empty file.
Thank you!
Your files are not in bed-format https://genome.ucsc.edu/FAQ/FAQformat.html#format1
But I have used the same format before and I got results:
chr22 StringTie exon 354097 359650 1000 + . gene_id "MSTRG.8010"; transcript_id "MSTRG.8010.1"; exon_number "1"; 1 475 5554 0.0855239
And the program is supposed to work with gff and gtf files as well.
Ok, it was not clear immediately that you are trying to run GTF file
Sorry, I should have explained better
And at my end, it works just fine..
chr19 StrAnA transcript 184909 186112 . + . gene_id "candidate_350" 1 463 1204 0.3845515
Did you edit a typo in the msg (Chr1 instead of Chromosome19)?
I had a space at the begining of chr in one of the files. I feel stupid now hahah.
Many thanks!
Silly mistakes do happen always. Genius is to recognize them :)
I've moved my comment as answer as essentially this resolves your problem.
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