Qualimap problem with Region.bed file

[AlliCox]

Hi everyone,

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 865591 865791 ref|SAMD11,ccds|CCDS2.2,ens|ENST00000420190,ens|ENST00000437963,ens|ENST00000342066,ens|ENST00000341065,ref|NM_152486,mRNA|AF161376,mRNA|AF161376,ref|NM_152486,ens|ENST00000341065,ens|ENST00000342066,ens|ENST00000437963,ens|ENST00000420190,ccds|CCDS2.2,ref|SAMD11

It's all on the same line - the 4th field is just long. I tried replacing all of the commas in the 4th field with tabs, but not all lines have enough entries in the 4th field to make up 6 fields.

Here is my question:
What should be in fields 4, 5, and 6 in the bed file? I'm used to seeing an identifier, +/- and something else (usually a null default value).

I got the bed file from the Agilent eArray SureSelect website.
Thanks,
Allison

[fennan]

Hi Allison,

Take a look to the: UCSC BED format definition

So in your case you can add default values to the 5th (score) and 6th (strand) fields of your bed file. For example this command could do it:

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