RNA-seq gff file cause MAKER running arrest

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

RNA-seq gff file cause MAKER running arrest

ytshen
Dears,

I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10).

 When I set the gff file as est_gff in  maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in  maker_opts.ctl file, the MAKER can run successfully.

Has this phenomenon happened to someone else? How I can fix it? Hope your reply!

Thank you very much!

Best!

Sinceraly,
Yanting


申妍婷
中国科学院遗传与发育生物学研究所
电话:010-64801362
地址:北京市朝阳区林萃东路1号楼
邮编:100101

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: RNA-seq gff file cause MAKER running arrest

Carson Holt-2
Cufflinks2gff is not a general GTF to GFF3 converter. It will work with cufflinks, but I don’t think it will convert Stringtie. Also if you are trying to use est2genome=1, it only works with fasta files.

—Carson


On Nov 29, 2018, at 8:24 PM, [hidden email] wrote:

Dears,

I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10).

 When I set the gff file as est_gff in  maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in  maker_opts.ctl file, the MAKER can run successfully.

Has this phenomenon happened to someone else? How I can fix it? Hope your reply!

Thank you very much!

Best!

Sinceraly,
Yanting


申妍婷
中国科学院遗传与发育生物学研究所
电话:<a href="tel:010-64801362" class="">010-64801362
地址:北京市朝阳区林萃东路1号楼
邮编:100101
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org