Question

Problem loading bamfiles to ChIPQC

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sergio.espeso-gil • 0

@sergioespeso-gil-6997

Last seen 4.2 years ago

New York

Hi,

I am trying to use ChIPQ, but it seems that my bamFiles are a bit different? I can not find the problem, I have tried to use a csv table and also a single sample and even using dba object from DiffBind , but I have always this error message:

[bam_index_load] fail to load BAM index.

Error: 16 errors; first error:

Error in value[[3L]](cond): failed to open BamFile: failed to load BAM index

I have a csv table with 16 samples. I guess is a problem with the index, should have indexed bam files then? any suggestion?

Thanks a lot!

Sergio

ChIPQC • 3.2k views

ADD COMMENT • link 9.3 years ago sergio.espeso-gil • 0

score 0 · Answer 1 · 2015-01-18

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Entering edit mode

sergio.espeso-gil • 0

@sergioespeso-gil-6997

Last seen 4.2 years ago

New York

Solved,

I have just indexed my samples, first sorting and after indexing as follows:

samtools sort filename.bam filename.sort

samtools index filename.sort.bam

Hope could be useful for other users.

Sergio

ADD COMMENT • link 9.3 years ago sergio.espeso-gil • 0

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Hi Sergio, Thank you for the post. You are right that ChIPQC requires a bam file to have index. We will add a feature to check bam is sorted and index a file if none are available. Best, tom On Sun, Jan 18, 2015 at 5:27 PM, sergio.espeso [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User sergio.espeso <https: support.bioconductor.org="" u="" 6997=""/> wrote Answer: > Problem loading bamfiles to ChIPQC > <https: support.bioconductor.org="" p="" 64185="" #64186="">: > > Solved, > > I have just indexed my samples, first sorting and after indexing as > follows: > > samtools sort filename.bam filename.sort > > samtools index filename.sort.bam > > Hope could be useful for other users. > > > > Sergio > > > > > > > > > > ------------------------------ > > You may reply via email or visit > A: Problem loading bamfiles to ChIPQC >

ADD REPLY • link 9.3 years ago Thomas Carroll ▴ 420