Extracting short sequences as FASTA
77 views
Skip to first unread message
Luke William Gent
Nov 7, 2023, 1:39:05 PM11/7/23
to gen...@soe.ucsc.edu
Hi!
I tried to copy what was instructed here:
'
'
I went to the table browser:
From what I gather I think I did what I needed correctly? But I'm sure I'm doing something wrong, what I did was for example was write in the region of interest ELOVL2 (that's my gene of interest), clicked look up, and clicked the relevant one. I think the rest of the settings are okay? However it just downloaded a gzip of a text file. I'm not sure if I can in fact get a FASTA file from this.
'
'I went to the table browser:
From what I gather I think I did what I needed correctly? But I'm sure I'm doing something wrong, what I did was for example was write in the region of interest ELOVL2 (that's my gene of interest), clicked look up, and clicked the relevant one. I think the rest of the settings are okay? However it just downloaded a gzip of a text file. I'm not sure if I can in fact get a FASTA file from this.
Essentially I would like to download FASTA.gz files of specific short sequences based on region of interests either via position or gene please. I'm sorry for being a pain. Is it easier via the FTP server?
Best,
Luke
Matthew Speir
Nov 11, 2023, 7:13:34 PM11/11/23
to Luke William Gent, gen...@soe.ucsc.edu
Hello, Luke.
Thank you for your question about downloading sequence in FASTA format from the UCSC Genome Browser.
If you unzip the gzip file, it will be a plain text file. It is just a compression algorithm that makes the file smaller which can be useful for downloading large amounts of sequence. Since you're downloading the sequence of a single gene, you could likely just select "plain text" as the output option.
Thank you for your question about downloading sequence in FASTA format from the UCSC Genome Browser.
If you unzip the gzip file, it will be a plain text file. It is just a compression algorithm that makes the file smaller which can be useful for downloading large amounts of sequence. Since you're downloading the sequence of a single gene, you could likely just select "plain text" as the output option.
If you want specific regions, not just a gene, you will need to use the custom track method as described in the FAQ you mentioned. If you are using that method, you'll need to be sure to select Group > Custom Tracks and Track > "Your Track Name" instead of the GENCODE track from your second screenshot.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
---
Matthew Speir
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/GV2PR03MB9428908AE9C5849BDCE09FDA90A9A%40GV2PR03MB9428.eurprd03.prod.outlook.com.
Reply all
Reply to author
Forward
0 new messages