BEDTools coverage or intersect

Question

[alvarocentron91]

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!

Answer 1

[Santosh Anand]

Your files are not in bed-format https://genome.ucsc.edu/FAQ/FAQformat.html#format1

[alvarocentron91]

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.

[Santosh Anand]

Ok, it was not clear immediately that you are trying to run GTF file

[Santosh Anand]

And at my end, it works just fine..

chr19   StrAnA  transcript  184909  186112  .   +   .   gene_id "candidate_350" 1   463 1204    0.3845515

[Santosh Anand]

Did you edit a typo in the msg (Chr1 instead of Chromosome19)?

[alvarocentron91]

I had a space at the begining of chr in one of the files. I feel stupid now hahah.

Many thanks!

[Santosh Anand]

Silly mistakes do happen always. Genius is to recognize them :)

I've moved my comment as answer as essentially this resolves your problem.

[alvarocentron91]

Sorry, I should have explained better