Error caused by alignments

[gaochengPRC]

Hi Jeff,

When I run the MethylAction, I get the error message below:

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Error in .local(x, use.names, use.mcols, ...) :
For some pairs in 'x', the 2 alignments are not on the same chromosome. Cannot associate a unique genomic range to such pairs. Please call granges() with 'on.discordant.seqnames="drop"' to drop these pairs, or with 'on.discordant.seqnames="split"' to represent each of them with 2 genomic ranges in the returned GRanges object. Note that in both cases the returned object won't be parallel to 'x'. Alternatively, please consider using grglist() instead of granges() to turn 'x' into a GRangesList object instead of a GRanges object. See ?GAlignmentPairs for more information.
Calls: getReads ... FUN -> as -> asMethod -> granges -> granges -> .local

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I have looked through the source code of getReads, however, I still have no idea about how to adapt your source code to my case. Do you have any specific instructions? Thank you in advance!

[jeffbhasin]

Hello, thanks for trying the software. I believe the error is caused because there are improperly paired reads present in the input BAM file (reads where one mate aligns to one chromosome and one to another). I would suggest filtering these out and only having properly paired reads before trying to run getReads(). Software like Picard Tools I believe could do this filtering.