Question

Using wig2array from iSeeRNA

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6.4 years ago

anu014 ▴ 190

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 • 1.1k views

ADD COMMENT • link updated 6.2 years ago by hellosunking • 0 • written 6.4 years ago by anu014 ▴ 190

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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.

ADD REPLY • link 6.4 years ago by anu014 ▴ 190

score 0 · Answer 1 · 2018-08-30

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.