Bedops --difference errors
0
0
Entering edit mode
4.7 years ago
rbronste ▴ 400

Hi

bedops --difference giving me some errors in the final bed file and Im wondering why, how to get a workaround?

chr8 9 69893500 5.00E+07 95000416 65834

Getting some intervals that look like this and not sure where its going off the rails when trying to subtract a genomic space from another interval file? Thanks!

Rob

ChIP-Seq bedops • 1.3k views
ADD COMMENT
0
Entering edit mode

Are your inputs sorted (i.e., with sort-bed)? Do you have files with Windows line endings (e.g., from Excel spreadsheets)? If you want to post your files somewhere, I'm happy to take a quick look.

ADD REPLY
0
Entering edit mode

I tried to sort immediately following bedops --difference with a file of CTCF coordinates in mm10 however get the following error message right after when I try to sort:

Error on line 67243 consensus_bedops_CTCFdiff.bed. Genomic end coordinate is less than (or equal to) start coordinate.

ADD REPLY
0
Entering edit mode

You should sort your input files (regions of interest and CTCF regions) with sort-bed before you do any set operations with bedops. You only need to sort once, but you need to make sure the inputs are sorted before you work on them.

ADD REPLY
0
Entering edit mode

Bedops sorting has been weird for me in general, often get this sort of error message:

BED row length exceeds capacity at line 1 in consensusPeaks_DiffBind_mm10.bed. Check that you have unix newlines (cat -A) or increase TOKENS_MAX_LENGTH in BEDOPS.Constants.hpp and recompile BEDOPS.

ADD REPLY
3
Entering edit mode

Are you working with Windows or Microsoft Office-sourced files? This can cause problems with Unix-based bioinformatics tools of all kinds, including BEDOPS. Here's one way to strip Windows newlines and sort the BED file in one pass:

\$ tr -d '\r' < bad.bed | sort-bed - > good.bed

ADD REPLY
1
Entering edit mode

Very infrequently I open something in excel but primarily work in through command line on a computing cluster. Though yes I may have stupidly polluted some of these. Thanks for the tip!

ADD REPLY

Login before adding your answer.

Traffic: 2211 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6