coverageBed giving unordered results at top of list

[yuchioj]

Hi all

So I wanted to use the following command to get the coverage of each exon of my exon sequencing data:

coverageBed -a <a.bed> -b <b.bed>

where a.bed is the one I got from my exon seq data and b.bed is from refseq from ucsc (both are focusing on one chromosome).

It gave a result as shown in the manual but the top part of the result list (~50 rows) are randomly picked out from the ordered positions from the refseq. Some of them are also duplicated in several lines. The rest part of the list looked all good.

Any idea why?

Thanks!

[dariober]

Hi all

So I wanted to use the following command to get the coverage of each exon of my exon sequencing data:

coverageBed -a <a.bed> -b <b.bed>

where a.bed is the one I got from my exon seq data and b.bed is from refseq from ucsc (both are focusing on one chromosome).

It gave a result as shown in the manual but the top part of the result list (~50 rows) are randomly picked out from the ordered positions from the refseq. Some of them are also duplicated in several lines. The rest part of the list looked all good.

Any idea why?

Thanks!

Hi,
Can you post the first ~100 lines fo your output?

I'm not sure in which order coveregeBed prints out the output, in any case that can be easily fixed with something like (to sort by chromosome and position):

coverageBed -a <a.bed> -b <b.bed> > coverage.bed
sort -k1,1 -k2,2n -k3,3n coverage.bed > coverage.sorted.bed

The duplicate lines might be present in your b.bed file?

Dario

[yuchioj]

Hi Dario

Thanks for your reply. The output for the first several lines (is interestingly different from the output yesterday but still has the problems):

http://dl.dropbox.com/u/34105617/Screen%20Shot%202012-10-24%20at%2010.45.59%20AM.png

The lines in b.bed are not duplicated.

Thanks!

Yuchio