diffHiC preparePairs error
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roladali ▴ 20
@roladali-9193
Last seen 5.1 years ago

Hello, 

I am trying to used diffhic to analyze my HiC data. I am getting an error when I use preparePairs:

 

preparePairs(samplename, hs.Dpn, file=paste(samplename, "h5", sep="."), dedup=TRUE, minq=10)

Error in (function (classes, fdef, mtable)  : 

  unable to find an inherited method for function ‘seqnames’ for signature ‘"NULL"’

 

I have made sure that hs.Dpn is a GRanges object with the proper cut sites. 

samplename is the name of the bam. I had tried to use the full path to the bam file but that did not work. I created a soft link to the file to avoid the full path but that didnt work. I copied the bam file to the current directory to avoid full paths or soft links but that didnt work either. 

I am assuming that the preparePairs method is not able to open the bam file correctly but I am not sure why. Please let me know what I am missing.

Thanks!

 

diffhic preparepairs • 583 views
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Aaron Lun ★ 27k
@alun
Last seen 1 hour ago
The city by the bay

If you read the documentation, you'll see that preparePairs expects a pairParam object, not a GRanges object.

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Thank you for answering that so gracefully (instead of perhaps pointing out how stupid that was on my behalf ;)).
I am actually following the documentation and I did create the pair param object but typed in the wrong object. I did correct it but I got another error:

 preparePairs(samplename, hs.param.Dpn, file=paste(samplename, "h5", sep="."), dedup=TRUE, minq=10)

Error in preparePairs(samplename, hs.param.Dpn, file = paste(samplename,  : 

  conversion table should have length equal to the number of chromosomes

 

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It means that there's more chromosomes in your fragment list than there are in the BAM file. Perhaps the function could be more forgiving; but for now, you'll have to manually remove the extra chromosomes.

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