Question: Gene length table from gtf file for rpkm() function
0
gravatar for debitboro
2.6 years ago by
debitboro110
Belgium
debitboro110 wrote:

Hi Biostars,

I have a RNASeq count table at gene level from HTSeq, and I want to get the gene length table from the used gtf file (from Ensembl) only for the genes in the HTSeq table. Is there anyway or some scripts to do this ?

ENSG00000000003 0 0 1 4 0 0 0 0 0 15 2 11 0
ENSG00000000419 2 2 3 3 14 20 9 13 37 81 13
ENSG00000000460 2 5 7 5 43 11 15 11 14 71 38
....
....

this is my HTSeq table, and I want to get the length only for ENSG00000000003, ENSG00000000419, ENSG00000000460, ...

ADD COMMENTlink modified 2.6 years ago by EagleEye6.2k • written 2.6 years ago by debitboro110
0
gravatar for EagleEye
2.6 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

You can get the length of individual genes using columns 4 and 3 of the files generated by following script,

https://github.com/santhilalsubhash/rpkm_rnaseq_count/blob/master/README.md

http://bioinformaticsonline.com/snippets/view/28043/rpkm-normalization-perl

http://bioinformaticsonline.com/snippets/view/28042/rpkm-normalization-r-script

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by EagleEye6.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 640 users visited in the last hour