How to merge annotation file(gtf) from different souce

Question

[lan_cat]

Hi, guys

I am doing RNA-seq data analysis. And this requires reference genome and annotation gtf file.

When I read papers, I found that they always integrate genome data and gtf file from different source (UCSC refSeq and ensemble), but there is little detail information about how to do it.

So my question is

1. how to integrate genome data(.fasta) from different sources(UCSC refSeq and ensemble)
2. how to integrate annotation data(.gtf) from different sources(UCSC refSeq and ensemble)

Thank you!

[Evgeniia Golovina]

Hi!

To merge annotations, you can use cuffmerge (part of Cufflinks).

You also maybe find the answer there --> How To Merge Contigs From Two Different Assembler :

[hirahameed222]

Can you please help me, How can I download reference genome of wheat (Triticum aestivum) as index for mapping (with RNA-seq) by HISAT2?

Answer 1

[Devon Ryan]

You don't need to bother with any of that. The Ensembl annotations are superior to those from UCSC, simply use them instead.