Problems importing GFFv3 Annotation into SeqMonk

jjw14 · 04-04-2012, 07:27 AM

I am using SeqMonk version 1.0 and trying to add annotation files in GFFv3 format available at ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/

Name Size Date Modified [parent directory]
ref_Sscrofa10.2_scaffolds.gff3.gz 13.3 MB 3/7/12 9:26:00 PM
ref_Sscrofa10.2_top_level.gff3.gz 13.0 MB 3/7/12 9:26:00 PM

When I import them into SeqMonk, receive the following error after selecting FILE --> IMPORT ANNOTATION --> GFF/GTF:

-----
Request Generated Warnings...

There were 530303 warnings when processing your request - showing the first 5000

Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
Couldn't find a chromosome called NC_010443.4
...

------

It seems that the first column should be a chromosome designation (e.g. Chr1), but the GFFv3 format does not have this information in column 1.

The SeqMonk changelog states that "Feature import from GFFv3 and GTF files" is supported, so I am not sure what my mistake is.

Can anyone please help me with this?
Thank you,
jjw14

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04-04-2012, 07:27 AM	#1
jjw14 Member Location: Missouri Join Date: Apr 2010 Posts: 39	Problems importing GFFv3 Annotation into SeqMonk I am using SeqMonk version 1.0 and trying to add annotation files in GFFv3 format available at ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ Name Size Date Modified [parent directory] ref_Sscrofa10.2_scaffolds.gff3.gz 13.3 MB 3/7/12 9:26:00 PM ref_Sscrofa10.2_top_level.gff3.gz 13.0 MB 3/7/12 9:26:00 PM When I import them into SeqMonk, receive the following error after selecting FILE --> IMPORT ANNOTATION --> GFF/GTF: ----- Request Generated Warnings... There were 530303 warnings when processing your request - showing the first 5000 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 Couldn't find a chromosome called NC_010443.4 ... ------ It seems that the first column should be a chromosome designation (e.g. Chr1), but the GFFv3 format does not have this information in column 1. The SeqMonk changelog states that "Feature import from GFFv3 and GTF files" is supported, so I am not sure what my mistake is. Can anyone please help me with this? Thank you, jjw14