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Question: htseq-count: Error processing GFF file
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gravatar for Nmojica
16 months ago by
Nmojica • 20
Nmojica • 20 wrote:

Hi!

I am running htseq-count for a RNA-seq and I got this error:

Fatal error: Unknown error occurred Error occured when processing GFF file (line 1 of file /galaxy-repl/main/files/020/629/dataset_20629796.dat): Failure parsing GFF attribute line [Exception type: ValueError, raised in __init__.py:164]

Here is a sample of what I got after I converted my data to .GFF:

seqname                 source feature start  end  score strand frame  attribute
TRINITY_DN95_c0_g1_i1   . Gene  1   220   0 .   .   gene_id "TRINITY_DN95_c0_g1_i1
TRINITY_DN44_c0_g1_i1   . Gene  1   232   0 .   .   gene_id "TRINITY_DN44_c0_g1_i1
TRINITY_DN44_c1_g1_i1   . Gene  1   203   0 .   .   gene_id "TRINITY_DN44_c1_g1_i1
TRINITY_DN54_c0_g1_i1   . Gene  1   311   0 .   .   gene_id "TRINITY_DN54_c0_g1_i1
TRINITY_DN0_c0_g1_i1    . Gene  1   404   0 .   .   gene_id "TRINITY_DN0_c0_g1_i

I don't know what is wrong. I am totally new to this and I would appreciate your help.

rna-seq • 1.0k views
ADD COMMENT • link •
modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by Nmojica • 20
1
gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tools in the group Text Manipulation can help with both changes. The first may be enough, but the second is odd formatting.

1) Remove the header line, it is not needed and probably the source of this particular error.

2) Remove the single "double quote". Meaning, change this:

TRINITY_DN95_c0_g1_i1   . Gene  1   220   0 .   .   gene_id "TRINITY_DN95_c0_g1_i1

to be 

TRINITY_DN95_c0_g1_i1   . Gene  1   220   0 .   .   gene_id TRINITY_DN95_c0_g1_i1

Thanks, Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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