Question: summarizeOverlaps 'sequences have incompatible seqlengths' errors
0
gravatar for krwyaong.ju
14 months ago by
krwyaong.ju0 wrote:

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 • 278 views
ADD COMMENTlink modified 14 months ago by Martin Morgan ♦♦ 23k • written 14 months ago by krwyaong.ju0

 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 It’s very out of date, and all of the material is copy-pasted from a very old version of our workflow, without prominent attribution or link to the primary source.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 REPLYlink modified 14 months ago by Martin Morgan ♦♦ 23k • written 14 months ago by Michael Love24k
Answer: Error: BiocParallel errors
0
gravatar for Martin Morgan
14 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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()).

ADD COMMENTlink written 14 months ago by Martin Morgan ♦♦ 23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 161 users visited in the last hour