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Question: DEXSeq Count files do not correspond to the flattened annotation file
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gravatar for rmf
9 weeks ago by
rmf0
rmf0 wrote:

Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be found on the F.A.Q. page.Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be found on the F.A.Q. page.

I get the following error when reading data using DEXSeqDataSetFromHTSeq.

dex <- DEXSeqDataSetFromHTSeq( 
  paths, meta, 
  design=~sample+exon+family:exon+condition:exon, 
  flattenedfile="dr.dexseq.gff")
Error in DEXSeqDataSetFromHTSeq(paths, meta, design = ~sample + exon +  : 
  Count files do not correspond to the flattened annotation file

The exon counts looks like:

ENSDARG00000000001:001 10
ENSDARG00000000001:002 14
ENSDARG00000000001:003 23
ENSDARG00000000001:004 5
ENSDARG00000000001:005 10

The flat gff looks like:

1 dexseq_prepare_annotation.py aggregate_gene 6408 12027 . - . gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6408 6641 . - . transcripts "ENSDART00000164359"; exonic_part_number "001"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6642 6643 . - . transcripts "ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "002"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6644 6760 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "003"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6892 6955 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "004"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6956 7335 . - . transcripts "ENSDART00000158290"; exonic_part_number "005"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 9558 9694 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000157701"; exonic_part_number "006"; gene_id "ENSDARG00000099104"

As far as I can see, everything looks fine. Any idea on what might be wrong? 

 

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by rmf0

Uff, sorry for the delay: I missed your message earlier. I hope this has been solved. If not, could you check if the number of lines on your count files corresponds to the number of lines contatining "exonic_part" in the third column of your annotation file?

ADD REPLYlink written 5 weeks ago by Alejandro Reyes1.5k
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