Question: How to compare CDS gff with genome guided assembled gff
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gravatar for Bioinfonext
2.0 years ago by
Bioinfonext140
Korea
Bioinfonext140 wrote:

I am working on plant species transcriptome. Its draft genome is known. We want to identify some new transcripts in genome-guided assembly.

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

rna-seq • 629 views
ADD COMMENTlink written 2.0 years ago by Bioinfonext140
1

I'm not familiar with RNAseq analysis. But according to your description, bedtools2 and bedops may help. gff can be converted to bed by gff2bed from bedops.

ADD REPLYlink written 2.0 years ago by shenwei3564.5k
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