Problem loading bamfiles to ChIPQC
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@sergioespeso-gil-6997
Last seen 20 months 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 • 2.1k views
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Entering edit mode
@sergioespeso-gil-6997
Last seen 20 months 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 

 

 

 

 

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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 >
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