Qualimap problem with Region.bed file

Question

[salvatore.digiorgio]

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

[finswimmer]

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

[salvatore.digiorgio]

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.

[salvatore.digiorgio]

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