Q1:
I want to say great job with the Pseudogene.org site! I recently noticed a potential error and wanted to send a email to inform you if you haven’t already picked it up yourselves….

In the file located at the following address:

http://www.pseudogene.org/psicube/data/gencode.v10.pgene.parents.txt

The start and end chromosomal locations for the pseudogenes are the same. See below:

ENST00000344844.3

unprocessed_pseudogene

chr19 +

9314984

9314984

ENSG00000237521.1 ENST00000456448.1 OR7E24

"Transcribed: 0" "Active Chromatin: GM12878=0;K562=0;Helas3=0;Hepg2=0;H1hesc=1"

"Open Chromatin: GM12878=0;K562=0;Helas3=.;Hepg2=.;H1hesc=."

"TFBS: GM12878=0;K562=0;Helas3=0;Hepg2=0;H1hesc=0"

"Pol2: GM12878=0;K562=0;Helas3=0;Hepg2=0;H1hesc=0"

"Constraint: 0"

ENST00000359901.3

unprocessed_pseudogene

chr2 –

98123508

98123508 . .

. "Transcribed: 0"

"Active Chromatin: GM12878=1;K562=0;Helas3=0;Hepg2=0;H1hesc=1"

"Open Chromatin: GM12878=0;K562=0;Helas3=.;Hepg2=.;H1hesc=."

"TFBS: GM12878=1;K562=1;Helas3=1;Hepg2=1;H1hesc=0"

"Pol2: GM12878=1;K562=1;Helas3=1;Hepg2=1;H1hesc=0"

"Constraint: 0"

ENST00000459808.1

processed_pseudogene chr3 –

136527393

136527393 ENSG00000198075.5 ENST00000272452.2

SULT1C4 "Transcribed: 0"

"Active Chromatin: GM12878=1;K562=0;Helas3=1;Hepg2=1;H1hesc=1"

"Open Chromatin: GM12878=0;K562=0;Helas3=.;Hepg2=.;H1hesc=."

"TFBS: GM12878=0;K562=0;Helas3=0;Hepg2=0;H1hesc=0"

"Pol2: GM12878=0;K562=0;Helas3=0;Hepg2=0;H1hesc=0"

"Constraint: 1"

A1:
Thanks for pointing us the problem. However, I’m a little confused of what file you are referring to. The parents file with url in your message (http://www.pseudogene.org/psicube/data/gencode.v10.pgene.parents.txt) does not match the contents you provided. The contents look more like from the file: http://pseudogene.org/psidr/psiDR.v0.txt. But neither file has the chromosome coordinates issue you mentioned. Maybe you meant some other file?

Q2:
It appears you are correct, i provided the link for the GENCODEv10 pseudogene resource instead of the v7 resource by mistake. I was, however, able to go back and find the file where I had found the mistake.

I had downloaded the Pseudogene Resource psiDR from the GENCODE website ( ftp://ftp.sanger.ac.uk/pub/gencode/psidr/psiDR.v0.txt.gz ) and assumed that this file is the same as the link you provide ( http://pseudogene.org/psidr/psiDR.v0.txt ). Although it appears they are not… The link on the GENCODE website ( ftp://ftp.sanger.ac.uk/pub/gencode/psidr/psiDR.v0.txt.gz ) displays the problem that I previously described, whereas the link you provide does not.

The file with the problem I described is actually linked at this page: http://www.gencodegenes.org/psidr/
Under the link entitled:
New! Pseudogene Resource psiDR
which redirects to: ftp://ftp.sanger.ac.uk/pub/gencode/psidr/psiDR.v0.txt.gz

I am not sure if you part of the administration for the GENCODE site or not, but potentially if you aren’t, you would like to contact them regarding the problem since it appears to be data from your lab that is represented.

I am sorry for providing the wrong link earlier. Please let me know if you have anymore trouble reproducing the problem.

A2:
I can see the problem too. I’ll contact GENCODE to have the file updated. Thanks for pointing this issue to us!