This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Using wig2array from iSeeRNA

Hello Biostars,

I want to identify lincRNAs from RNA-Seq data. For this purpose, first I ran cufflinks which gave me GTF to enter into iSeeRNA which in turn asked me to enter .conf file. For .conf file, I need to have .array file also.

So can anyone tell me how to create .array file using wig2array if I have just FASTA file? or can anyone tell me how to create .array file from scratch?

Please suggest me. Thanks :)

rna-seq genome next-gen
• 1,505 views • link
updated by hellosunking • hellosunking • written by anu014 anu014

My problem is partially solved. As right now I wanted to work on mm10. But how to do the same for hg38? iSeeRNA just has in-bulit files for hg19/mm9/mm10.

• 1 views • link
written by anu014 anu014

1 answer

Hi anu014,

I am Ahfyth, the author of iSeeRNA. I am sorry that we do not support hg38 yet and we will work on it.

To your question, the .array files are translated from PhastCons wiggle files. If you are working on hg38, you can download these files from UCSC Genome browser:

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons30way/hg38.30way.phastCons/

But you need to re-train a model with these files.

For more information, you can refer to the README file in the package.

• 1 views • link
written by hellosunking • hellosunking

Log in to answer this question.

More posts like this