problem for DEXseq

[wilburnguo]

dear sir, when i used the function, DEXSeqDataSetFromFeatureCounts(), i got the error :Error in DEXSeqDataSetFromFeatureCounts("results.txt", flattenedfile = flattenedfile, : Count files do not correspond to the flattened annotation file my code followed: source("~/biosoft/Subread_to_DEXSeq-master//load_SubreadOutput.R") genotype<-read.table('~/gse132508/data/genotype.txt',header = T) flattenedfile<-'~/alzheimer/annotation/dexseq_counts.gff' samp <- data.frame(row.names = genotype$Run, condition = genotype$LibrarySource) dxd.fc <- DEXSeqDataSetFromFeatureCounts("results.txt", flattenedfile = flattenedfile,sampleData = samp) all the file used here are following your support funtion,dexseq_prepare_annotation2.py,

[Polyalineli]

For me changing 255 to 254 in substr(aggregates$gene_id,1,255) line of DEXSeqDataSetFromFeatureCounts() solved the issue. Because in my case featurecounts cropped aggregate geneIDs of massively overlapped exons to 254 characters.

[LorenzoLF]

Same problem for me. Unfortunately changing 255 to 254 in substr(aggregates$gene_id,1,255) does not seem to fix it either. Has somebody found another fix? Thank you.