UCSC Fasta files by chromosome for rn6

Question

[AB]

Hi,

Ive noticed UCSC downloads page has fasta files by chromosome for hg19 and mm9. But that isn't available for rn6. Is there some place from where i can download fasta files by chromosome for rn6 genome assembly ?

Apoorva

Answer 1

[genecats.ucsc]

The UCSC utility twoBitToFa can get the sequence for an individual chromosome at a time via the -seq option, which you can run in a loop for each chromosome:

$ wget  http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.chrom.sizes
$ for chr in $(cut -f1 rn6.chrom.sizes); do twoBitToFa -seq="${chr}" http://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.2bit $chr.fa; done
$ # verify with the faSize util:
$ head -1 rn6.chrom.sizes
chr1    282763074
$ faSize chr1.fa
282763074 bases (14711797 N's 268051277 real 153502700 upper 114548577 lower) in 1 sequences in 1 files
%40.51 masked total, %42.73 masked real

You can download twoBitToFa and faSize from the following the directory appropriate for your operating system here: http://hgdownload.soe.ucsc.edu/admin/exe/

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: [e-mail]
• Questions involving private data: [e-mail]
• Questions involving mirror sites: [e-mail]

ChrisL from the UCSC Genome Browser

[GenoMax]

@ChrisL: Do you know why *.chromFa.tar.gz (assembly sequence in one file per chromosome.) are not made available for all genomes at UCSC? They are for human genome.

[genecats.ucsc]

We make these individual chromosome files when the chromosome count is under 100. Most assemblies these days have over 100 chromosomes and so we don't run them up anymore.

Answer 2

[cpad0112]

FYI, NCBI Rno6 chromosome wise sequences are available at: ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ and ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/Assembled_chromosomes/seq/

Answer 3

[Pierre Lindenbaum]

download from http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz and split by file: e.g: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File

[AB]

Thank you very much

Apoorva