Question: Comparing two gff/gtf files : de novo transcripts v/s reference
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gravatar for Abhishek Pratap
8.0 years ago by
United States
Abhishek Pratap170 wrote:
Hi All I am wondering if people based on their experience could share what methods one could use to compare two gff/gtf files. The reason why I want to do so is that we have constructed a RNA-Seq based transcriptome and would like to compare it with reference transcriptome we had from in-silico approaches. Ideally we are looking to find out 1. new genes we see 2. transcripts where the start/end side is changed (upstream/downstream) 3. possible gene fusions may be because in-silico approaches were not correct I know some of these could be resolved with BedTools but just wondering if Bioconductor has anything specific built in coz each time it pleasantly surprises me. Thanks! -Abhi [[alternative HTML version deleted]]
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