Invalid feature coordinates

[TheRealSmithLab]

Hi there!

There seem to be some inconsistencies with several entries in the CHESS2.2 gffs. Running gffread on the files flagged several entries with incompatible exon coordinates. For example:

Error: invalid feature coordinates (end<start!) at line: chr1 FANTOM exon 96813276 96813253 . + . Parent=CHS.2297.45

The output of grep CHS.2297.45 chess.gff further highlights the problem:

chr1 FANTOM transcript 96812803 96813405 . + . ID=CHS.2297.45;Parent=CHS.2297;FANTOM_coding_status=noncoding;STATUS=known_fantom;ASSEMBLED=yes;FANTOM_functional_evidence=3;FANTOM_rnacode_call=yes;FANTOM_phylocsf_call=yes chr1 FANTOM exon 96812803 96813106 . + . Parent=CHS.2297.45 chr1 FANTOM exon 96813276 96813253 . + . Parent=CHS.2297.45

[alevar]

Hi! Thank you for noticing the issue and bringing it to our attention! The versioning on the github repository was a little outdated and the more recent builds of the database have the issue corrected. We have now synced the latest release files between the webpage and the github repository.

Please let us know if you notice any other inconsistencies!

Best,

Ales

[xue-222]

Did you solve the problem?

[alevar]

Hi! Yes, the problem has been resolved in more recent builds. Furthermore, we have now release a major revision to the Database (CHESS 3) based on complete re-evaluation of the GTEx data, using updated tools and a more informed filtering process (as well as many other improvements).

[TheRealSmithLab]

Thank you Ales! I will sleep (mildly) better tonight :-)

On Fri, Apr 28, 2023, 2:58 p.m. Ales Varabyou @.***> wrote:

Closed #4 https://github.com/chess-genome/chess/issues/4 as completed.

— Reply to this email directly, view it on GitHub https://github.com/chess-genome/chess/issues/4#event-9127633321, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO3WASHPU3IXK23VMXCB65LXDQHNLANCNFSM453JJSMA . You are receiving this because you authored the thread.Message ID: @.***>