Question: UCSC Fasta files by chromosome for rn6
1
gravatar for Apoorva
3.0 years ago by
Apoorva260
United States
Apoorva260 wrote:

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

ucsc rn6 fasta • 1.8k views
ADD COMMENTlink modified 3.0 years ago by genecats.ucsc580 • written 3.0 years ago by Apoorva260
2
gravatar for genecats.ucsc
3.0 years ago by
genecats.ucsc580
genecats.ucsc580 wrote:

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: genome@soe.ucsc.edu
  • Questions involving private data: genome-www@soe.ucsc.edu
  • Questions involving mirror sites: genome-mirror@ose.ucsc.edu

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 3.0 years ago by genecats.ucsc580

@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.

ADD REPLYlink written 3.0 years ago by genomax91k

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.

ADD REPLYlink written 3.0 years ago by genecats.ucsc580
2
gravatar for cpad0112
3.0 years ago by
cpad011214k
India
cpad011214k wrote:

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/

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by cpad011214k
1
gravatar for Pierre Lindenbaum
3.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink written 3.0 years ago by Pierre Lindenbaum131k

Thank you very much

Apoorva

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Apoorva260
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