Obtain the BED file of Hepatitis C virus

Question

[lengocthien]

Dear everyone,

I am a newbie in studying bioinformatics. I would like to get the BED file of HCV in order to analyzing data by IGV, could you please show me how can I get it? More detailed information more useful for me, ex: where I start (NCBI, UCSC?..) and how I get the file?

I am very upset for not finding it, please help me!

Thanks in advance for any suggestions.

Cheers.

[Devon Ryan]

For viruses you'd be best off with either NCBI or JGI. I'm not sure how easy it is to get a BED or GTF file, you might have to get the genbank file from NCBI and convert it.

Edit: Right, it's a virus, so the number of genes/features is small enough that it's faster to just type out a BED file while looking at the Genbank file (e.g., this) than it is to bother with converting it.

[lengocthien]

Thanks, but on UCSC, I could only download the BED file of hg19, not virus. Where can I find the way?

[GenoMax]

See if this script gets you the BED file. You will need genbank format file for HCV.

[Devon Ryan]

You're replying to someone else's comment (that seems to have been removed), not mine.

[lengocthien]

Thanks, but on UCSC, I could only download the BED file of hg19, not virus. Where can I find the way?

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing comments. This allows threads to remain logically organized.

[GenoMax]

Did you not see the Edit that @Devon added to the comment above?

Answer 1

[pld]

Welcome to working with viruses in the human/mouse centric world of bioinformatics! The answer to your question is that there isn't one, and there probably won't ever be one.

ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/

There are several HCV entries here, they have GFFs, but not BED files. You can use bedops to convert the GFF to a BED.

A word of warning, the GFF files (for viruses) from NCBI tend to be poor quality and to a VERY limited range of genotypes/isolates. I've had plenty of issues with GFF files from NCBI not working with a range of tools. So you're often left to your own devices and a fair amount of manual editing. As others have said, and from personal experience, just making the file manually tends to be far easier. Thankfully this is a ssRNA virus, so you're not going to have a relatively huge genome like a poxvirus...

[lengocthien]

Thanks for your opinion, Joe!

Answer 2

[istloui1]

Where do I get HIV1 genome? I need to create .BED file.