Question: Finding S. cerevisiae mRNA of specific genes from SGD db.
0
gravatar for elisheva
11 weeks ago by
elisheva70
Israel
elisheva70 wrote:

Hi everyone! I have a problem with finding S. cerevisiae mRNA.
I have a list of genes names from SGD. For example a few genes
Q0275 Q0297 YAL039C YAL062W YAL063C
And I have to download all their mRNAs into 1 fata file .
I Did it so far using RefSeq db on the table browser.
But now, because it is another db I can't just upload the list and get the mRNA as I did before.
I also tried to download from SGD coding RNA and then compare the genes Ids.
(I got the genes Ids using YeastMine)
But unfortunately these are not the same Ids.
Thanks a lot!!

assembly sgd mrna • 198 views
ADD COMMENTlink modified 11 weeks ago by genomax39k • written 11 weeks ago by elisheva70

What do you mean you can't download sequence from SGD (e.g. YAL063C which is also called FLO9).

ADD REPLYlink written 11 weeks ago by genomax39k

If it wasn't clear: I have a list of genes and I want to download all their mRNAs into 1 fasta file.
I'ts about 600 genes, so I can't do it manually.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by elisheva70
2
gravatar for genomax
11 weeks ago by
genomax39k
United States
genomax39k wrote:

Get the sequence of all ORF's from here. Then use faSomeRecords from Kent Utilities from UCSC (with your ID's of interest in a file, one ID per line) to extract those 600 fasta files. faSomeRecords orf_coding_all.fasta file_w_id extracted.fa

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by genomax39k

Thanks a lot.
I am not familiar with this tool.
How can I run it from the command line? I can't open it.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by elisheva70

I gave you the example command line above.

ADD REPLYlink written 11 weeks ago by genomax39k

I know, but I am trying it and i get: Permission denied.
Should I install this tool or something like this? I downloaded it but it's a executable file.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by elisheva70
1

You don't need to install since it is a stand alone executable. All you should need to do is make the file executable by doing chmod u+x faSomeRecords and then run it ./faSomeRecords orf_coding_all.fasta file_w_id extracted.fa

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by genomax39k

It works now, Thanks!!

ADD REPLYlink written 11 weeks ago by elisheva70
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