Question: Qualimap problem with Region.bed file
0
gravatar for salvatore.digiorgio
2.1 years ago by
ITALIA-FIRENZE-
salvatore.digiorgio10 wrote:

I am trying to use an Agilent SureSelect exome enrichment bed file in Qualimap. When I run qualimap with the bed file (analyzing a bam), it says that the bed file should have six fields. Here is a sample line from the bed file:

chr1    3206095 3207055 gb|AY534250,ens|ENSMUST00000070533,ref|NM_001011874,entg|Xkr4,ccds|CCDS14803.1,gb|BC169294

I used bed file format on UCSC BED file definition and I modified my file using follow command line:

awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$4,0,"."}' orig.bed > new.bed

Nothing change, qulimap doesn't work. The error message is:

BED format error, bed file should have six fields. Problematic line: browserpositionchr1:3206095-3207055.

Thanks Salvatore

sequencing alignment • 878 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by salvatore.digiorgio10
1

Are you sure that you took the correct file (for the awk command and/or in qualimap)?

Open your new.bed and have a look whether browserpositionchr1:3206095-3207055 exists there.

EDIT: Wait, in the bed file I have here provided by Agilent, the first two line contain something like comments (unfortunately not introduced by a #). Just remove them.

fin swimmer

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by finswimmer14k

Yes, it could be first issue, another could be that column n 4 of bed file has \n at the end of line, my awk command line doesn't remove \n. I will try to adjust these things and i will see.

ADD REPLYlink written 2.1 years ago by salvatore.digiorgio10

The issue is comments not introduced by # and dos line ending !!!

ADD REPLYlink written 2.1 years ago by salvatore.digiorgio10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1726 users visited in the last hour