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How to merge annotation file(gtf) from different souce

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!

rna-seq
• 5,316 views • link
updated by Ram Ram • written by lan_cat • lan_cat

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

• 1 views • link
updated by Ram Ram • written by hirahameed222 • hirahameed222

1 answer

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

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

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