I wanted to check this file for check gene expression but the gene and transcript id are starting from 1000

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6.5 years ago

Ankur B. Sharma ▴ 20

Hi Guys, I am new here and I am trying to analyse one ENCODE data set. I have gene quantification file with an extension of .tsv I wanted to check this file for check gene expression but the gene and transcript id are starting from 1000 I am new in bioinformatics but I am trying to learn. please suggest me how to proceed with it. You can see the picture in the below-mentioned link. Hoping to get a response soon.

https://ibb.co/hQZDMT

encode gene expression RNA-seq rna-seq • 1.1k views

ADD COMMENT • link 6.5 years ago by Ankur B. Sharma ▴ 20

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please, describe your problem. We cannot understand:

I wanted to check this file for check gene expression but the gene and transcript id are starting from 1000

what do you want to check ? why 'starting from 1000' could be a problem ?

see How To Ask Good Questions On Technical And Scientific Forums

ADD REPLY • link 6.5 years ago by Pierre Lindenbaum 164k

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You should check the ENCODE page (or rather the pipeline they used) for a refererence to these arbitrary gene IDs, so genomic/transcriptomic positions. Without any reference, your file is pretty much useless (IMHO this is another great example why I never download anything but the rawest of the raw data from ENCODE and process them myself).

ADD REPLY • link 6.5 years ago by ATpoint 85k

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