Search
Question: DEXSeq Count files do not correspond to the flattened annotation file
0
gravatar for rmf
10 days 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 10 days ago • written 10 days ago by rmf0
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 2.2.0
Traffic: 183 users visited in the last hour