Question: Bedtools multicover how to submit a bam list
0
gravatar for benoit.tessoulin
3.3 years ago by
benoit.tessoulin30 wrote:

Hi,

I'm trying to use bedtools muticov to find out Copy Number Variations among my samples, using the CANOES soft. I got many bam samples and canno't figure out how to "impute" a list of bams to bedtools multicov.

Already tried the following

``

find *.bam | xargs bedtools multicov -bed probes.bed -q 20 > canoes.reads.txt

An other way around:

find *.bam > bam.list
bedtools multicov -bams bam.list -bed probes.bed -q 20 > canoes.reads.txt

CANOES tutorial suggests the following form, but I can't understand how a quote around bam list could enhance things.

bedtools multicov -bams `cat bamlist.txt` -bed probes.bed -q 20 > canoes.reads.txt

Thank you eveyone!

bedtools • 1.2k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by benoit.tessoulin30
1

but I can't understand how a quote around bam list could enhance things

The ` (backtick) causes the system command to run with the output being passed to program. They are there for a reason.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax85k

Thanks I got it for the backtick, but still doesn't do the job here...

ADD REPLYlink written 3.3 years ago by benoit.tessoulin30

And what's wrong with just following the tutorial? :-P

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

hehe, it doesn't work when I follow the tutorial :-P Gonna ask to bedtools team if it's bedtools' version issue. But i'm still surprised that other way around don't make it work out.

ADD REPLYlink written 3.3 years ago by benoit.tessoulin30
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