Question: How to merge annotation file(gtf) from different souce
0
gravatar for lan_cat
3.8 years ago by
lan_cat0
China
lan_cat0 wrote:

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!

myposts rna-seq • 1.8k views
ADD COMMENTlink modified 3.8 years ago by Devon Ryan90k • written 3.8 years ago by lan_cat0

Hi!

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

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

ADD REPLYlink written 3.8 years ago by Evgeniia Golovina980

Can you please help me, How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping (with RNA-seq) by HISAT2.

ADD REPLYlink written 4 months ago by hirahameed2220
3
gravatar for Devon Ryan
3.8 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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

ADD COMMENTlink written 3.8 years ago by Devon Ryan90k
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