BedTools intersect - Segmentation fault

Question

[Maria333]

Hi,

Has anyone experienced the "segmentation fault" error while trying to use bedtools intersect option? I am trying to see overlap exons between 2 bed files but I'm getting this error all the time. Any help will be much appreciated.

Thank you

[biocyberman]

Output of three commands: ẁhich bedtools, bedtools --version and uname -a could be helpful to know about your setup

Answer 1

[GouthamAtla]

If you are working with very large files, sort the bed files based on Chr and then Pos. sort -k1,1 -k2,2n and then use -sorted option.

From the manual:

-sorted For very large B files, invoke a "sweeping" algorithm that requires position-sorted (e.g., sort -k1,1 -k2,2n for BED files) input. When using -sorted, memory usage remains low even for very large files

If you still face the problem, split the files by Chr and then try to run the program at chromosome level. Otherwise provide more details about your data and post the exact error

[Maria333]

Thank you very much for that, it helped a lot. I sorted the bed file and then used sort -k1,1V to reverse the order so it is in ascending order.. Now I get the error:

Error: The genome file sorted.bed.ascending has no valid entries. Exiting.

Do you know why is this? The files seem fine now..

Thank you once again!

[GouthamAtla]

can you post few lines from your files ?

Answer 2

[Alex Reynolds]

Another option:

$ sort-bed exons1.bed > sorted_exons1.bed
$ sort-bed exons2.bed > sorted_exons2.bed
$ bedops --element-of 1 sorted_exons1.bed sorted_exons2.bed > exons1_that_overlap_exons2.bed
$ bedops --element-of 1 sorted_exons2.bed sorted_exons1.bed > exons2_that_overlap_exons1.bed