Question: csv into genome browser
0
gravatar for H.Hasani
4.8 years ago by
H.Hasani980
Freiburg, Germany
H.Hasani980 wrote:

Dear Biostars,

this might be a simple question, I'm looking for a way to convert my csv files into an acceptable format, so that I can visualize my data in genome browser. Moreover, my csv files are the simplified version of annotated output, therefore, I hope I can visualize the AA change, Consequence, & additional flag (e.g. sample ID).

Any advise would be highly appreciated

Edit: I realized that my question is very vague. Maybe the first is first! Is there anyway to convert csv files into vcf ?

Thanks!

snp genome browser • 2.1k views
ADD COMMENTlink modified 4.4 years ago • written 4.8 years ago by H.Hasani980
1

A csv file can contain anything. What kind of data are you talking about? single nucleotide variants/insertions & deletions, copy number, chipseq, methylation?

ADD REPLYlink written 4.8 years ago by Irsan7.3k

The csv file contains only annotated SNVs e.g. Gene, CHROM, POS, ID, AA, Consequence, Flag

ADD REPLYlink written 4.8 years ago by H.Hasani980

Then make sure you have a VCF file, because that is the standard format for SNVs. IGV can import and visualize VCFs.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Irsan7.3k

That was the reason for asking the original question! I could not find a way to convert csv to vcf particularly.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by H.Hasani980

I realized that my question is very vague. Maybe the first is first! Is there anyway to convert csv files into vcf ?

You realized this after 4 months and chose to edit the original post or is there a new question in there somewhere?

I see that you added an answer below as well :-)

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by GenoMax96k

No! The realization came right after receiving the first comments. To keep the original question intact I added lines after the "edit". This way people who answered and those who stop by, as yourself, still can follow this thread.

Few days ago, I added the answer that I learnt and back then did not know about. I thought it might be of interest to someone else.

By the way, accepting my own answer did not give me extra credit :)

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by H.Hasani980
1
gravatar for Jean-Karim Heriche
4.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

You could try genoverse, I think it can read CSV files.

ADD COMMENTlink written 4.8 years ago by Jean-Karim Heriche24k

Looks interesting, I'll try it. Thanks!

ADD REPLYlink written 4.8 years ago by H.Hasani980
0
gravatar for H.Hasani
4.4 years ago by
H.Hasani980
Freiburg, Germany
H.Hasani980 wrote:

For those who were looking for similar approach, I found that Personal Genome SNP format is the closest thing to my needs, as the AA change will be automatically linked to each SNP once it is correctly uploaded.

ADD COMMENTlink written 4.4 years ago by H.Hasani980
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