How can I download the fasta file of RepeatMasker UCSC table directly?

Question

[jonessara770]

Hi,

I am a newbie in Retrotransposable/repeat elements analysis.

I used UCSC table in order to get the sequence of RepeatMasker table in fasta format. When I download it through the webpage, the file is truncated at chr16 and does not have all chromosome.

How can I download the fastq file of RepeatMasker UCSC table directly?

Thanks Sara

[GenoMax]

fastq file of RepeatMasker UCSC table

Is that correct? I don't recollect there being an option to download fastq format files from table browser.

[GenoMax]

Tagging: genecats.ucsc

See the error below.

Answer 1

[mbk0asis]

I don't think you can download repetitive sequences directly from UCSC genome browser as genomax mentioned. Instead, get the bed file of RepeatMasker and whole genome sequence of your organism from UCSC genome browser, and use 'bedtools getfasta' to extract the sequences of retroelements.

[GenoMax]

You should be able to get the sequence using table browser (which is what OP was doing). It appears that their connection timed out and the entire file did not download.

[jonessara770]

Thanks! I tied this but the file is truncated.

[GenoMax]

Did you provide a file name to save the data to a file (rather than have to show up in the browser window)? If not try that.

[jonessara770]

Yes, I did and I save the file but it is truncated from chr18 upwards.

[GenoMax]

You are right in that the download from table browser is truncated after a certain length (I got a 1.6G file). You may want to get individual files for the remaining chromosomes and append them to the main.

It may be worth reporting this as a bug to UCSC support people. I will tag them here as well.