Question

summarizeOverlaps 'sequences have incompatible seqlengths' errors

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krwyaong.ju • 0

@krwyaongju-15652

Last seen 6.0 years ago

I follow the tutorial; RNA-Seq differential expression work flow using DESeq2 (http://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2).

I've got stuck below; Could you figure it out?

> library( "GenomicAlignments" )
> se <- summarizeOverlaps( exonsByGene, BamFileList( bamFiles ), mode="Union",
+   singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE )
Error: BiocParallel errors
  element index: 1, 2, 3
  first error: sequences 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y have incompatible seqlengths:
  - in 'x': 248956422, 242193529, 198295559, 190214555, 181538259, 170805979, 159345973, 145138636, 138394717, 133797422, 135086622, 133275309, 114364328, 107043718, 101991189, 90338345, 83257441, 80373285, 58617616, 64444167, 46709983, 50818468, 156040895, 57227415
  - in 'y': 249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566
>

deseq2 • 962 views

ADD COMMENT • link updated 6.0 years ago by Martin Morgan 25k • written 6.0 years ago by krwyaong.ju • 0

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Entering edit mode

I’d recommend not following that guide/website. It’s very out of date, and all of the material is copy-pasted from a very old version of our workflow, without prominent attribution or link to the primary source. The up-to-date workflow is here:

https://bioconductor.org/packages/rnaseqGene

ADD REPLY • link updated 6.0 years ago by Martin Morgan 25k • written 6.0 years ago by Michael Love 41k

score 0 · Answer 1 · 2018-05-10

It's not a BiocParallel error, but looks instead like your bam files result from alignment to one genome and your exonsByGene from alignment to another genome. The solution is to create exonsByGene from the correct genome. It might also help to use summarizeOverlaps on a subset of your data (e.g., smallest BAM file) and to debug using 'serial' rather than parallel mode BiocParallel::register(BiocParallel::SerialParam()).