How to compare CDS gff with genome guided assembled gff

[Yogesh Gupta]

Dear All,

I am working on transcriptome. The draft genome is known. We want to identify some new transcripts in genome-guided assembly of RNAseq data.

I need your help to remove overlapping sequencing by comparing already reported CDS gff file with assembled transcript gff file using StringTie.

Can we also remove the redundancy of transcript which mapping to the same location on the genome by using gff file.

Thanks

Yogesh Gupta

Postdoctoral Researcher

[Chris Villarreal]

Dear Yogesh Gupta,

Thank you for your question, but it appears it falls outside the scope of this mailing list as you are inquiring about the usage of an external tool. However, if I understand what you need correctly you can use our tools to convert GFF to a BED then remove overlaps. Here is a previously answered mailing list question with that information: 

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/gff$20to$20bed/genome/SQ5QebQ7XPI/NVxuWxH5UAIJ

This question pertains to removing overlaps: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/remove$20overlapping$20intersection$20bed/genome/BJ-6DlaZNCY/grgGIpuJAwAJ.

Additionally, it appears that StringTie offers utilities that may assist you. Here is gffcompare: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare.

We also recommend that you post this question in a forum like BioStars, https://www.biostars.org/, where scientists may be able to provide you with the scientific direction you need.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

-Chris V

UCSC Genome Browser

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