Question: summarizeOverlaps 'sequences have incompatible seqlengths' errors
0
17 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 • 349 views
modified 17 months ago by Martin Morgan ♦♦ 23k • written 17 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 It’s very out of date, and all of the material is copy-pasted from a very old version of our workflow, without prominent attribution or link to the primary source.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 17 months ago by Martin Morgan ♦♦ 23k • written 17 months ago by Michael Love25k
0
17 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()).