GFF3 to RefFlat for non UCSC genomes

[aner]

Dear all
I need to convert GFF3 files to RefFlat; or to find how to generate RefFlat files. The reason for my question is that I need to run Picard, module CollectRnaSeqMetrics, that requires RefFlat files.

I am working on Arabidopsis Thaliana, that is not in UCSC database. This means that I cannot use UCSC RefFlat files but I have to generate them.

UCSC provides a program that seems to cope with my need: gff3ToGenePred (link: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred). In this case the program does not work with the available GFF3 for my genome, TAIR10 (this link for original GFF3 Tair10: ftp://ftp.arabidopsis.org/home/tair/...GFF3_genes.gff and ftp://ftp.arabidopsis.org/home/tair/...ransposons.gff) because of GFF3 errors: GFF3 files seem not standard GFF3.

For this reason I am also trying to find a GFF3 validator but I only found online validators that do no work.

Can anyone help me on creating a RefFlat file for genomes that are not in UCSC database?

Thank you
Andrea

[aner]

Ok, problem solved! This is my way:

1. download your GFF3 file from ftp://ftp.ensemblgenomes.org/pub/ (I found also TAIR10 files here)
2. download gff3ToGenePred from UCSC web site
3. run gff3ToGenePred to convert your file to GenePred file format (= refFlat)
4. run Picard CollectRnaSeqMetrics with this reference refFlat file.

Done ;-)

[steven]

Ok, problem solved! This is my way:

1. download your GFF3 file from ftp://ftp.ensemblgenomes.org/pub/ (I found also TAIR10 files here)
2. download gff3ToGenePred from UCSC web site
3. run gff3ToGenePred to convert your file to GenePred file format (= refFlat)
4. run Picard CollectRnaSeqMetrics with this reference refFlat file.

Done ;-)

Thanks for letting everyone know, I was curious about that question. So, was that because of a difference between the TAIR GFF3 annotations from UCSC and the one from Ensembl?

[aner]

was that because of a difference between the TAIR GFF3 annotations from UCSC and the one from Ensembl?

No; I did not find GFF3 files of my genome (Arabidopsis Thaliana) into UCSC so I needed to download GFF3 files from another source. Using TAIR10 official web site, the processed GFF3 file (using UCSC gff3ToGenePred) returned errors (formatting errors). I tried to find a valid file before creating it myself, so that I could use that site for all future cases, and I found ensemblgenomes for this purpose.

[aner]

PS: I could run Picard (version 1.51) CollectRnaSeqMetrics but the option CHART did not work... so I have to understand why...

[steven]

No; I did not find GFF3 files of my genome (Arabidopsis Thaliana) into UCSC so I needed to download GFF3 files from another source. Using TAIR10 official web site, the processed GFF3 file (using UCSC gff3ToGenePred) returned errors (formatting errors). I tried to find a valid file before creating it myself, so that I could use that site for all future cases, and I found ensemblgenomes for this purpose.

Yes, right, I meant TAIR (no Arabidopsis in UCSC). So the GFF3 from Ensembl worked but not the original one from TAIR.. interesting.

[johnny_273]

Help!!!

Dear all
I need to convert GFF3 files to RefFlat; or to find how to generate RefFlat files. The reason for my question is that I need to run Picard, module CollectRnaSeqMetrics, that requires RefFlat files.

I am working on Arabidopsis Thaliana, that is not in UCSC database. This means that I cannot use UCSC RefFlat files but I have to generate them.

UCSC provides a program that seems to cope with my need: gff3ToGenePred (link: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred). In this case the program does not work with the available GFF3 for my genome, TAIR10 (this link for original GFF3 Tair10: ftp://ftp.arabidopsis.org/home/tair/...GFF3_genes.gff and ftp://ftp.arabidopsis.org/home/tair/...ransposons.gff) because of GFF3 errors: GFF3 files seem not standard GFF3.

For this reason I am also trying to find a GFF3 validator but I only found online validators that do no work.

Can anyone help me on creating a RefFlat file for genomes that are not in UCSC database?

Thank you
Andrea

HELP!!! my research need me to do sth similar with "anner" or "steven".
But I couldn't find gff3 file of arabidopsis on the ftp address "anner" give

[johnny_273]

my email address is [email protected]
Please help!!!
I need proper .gff3 file of arabidopsis that could be recognized and worked out with
gff3ToPred program.

[aner]

hi Johnny
use this file:

ftp://ftp.ensemblgenomes.org/pub/rel...psis_thaliana/

then (since it is GTF), instead of gff3ToPred, use gtfToPred:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred

Tell me if this is working now.

[johnny_273]

I Love You, anner!!!

hi Johnny
use this file:

ftp://ftp.ensemblgenomes.org/pub/rel...psis_thaliana/

then (since it is GTF), instead of gff3ToPred, use gtfToPred:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred

Tell me if this is working now.

It's great, Saving me lots of time and energy.
I used to think that I have to change formats of gff3 file if using the gff3ToPred program... It's quite easy in your way.
Be my friend and let me know if there is anything I could help.

[aner]

;-) It is good to know that my suggestions led you to your results!! The real meaning of a network!