Question: Reference mouse genome
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gravatar for atheeth14
7 months ago by
atheeth140
atheeth140 wrote:

I wish to align my mouse WES fastq files using a GRCM38 reference genome. I found the genome in the USNC portal (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/snp142Mask/). However, the fasta files are available for individual chromosomes as far as I understand. How/where to get the WES fasta file for mus musculus? Also, once aligned, I wish to annotate the variants using snpEff. But the GRCm38 genome in their database is a different version (CRCm38.75). Will this cause 'ERROR_CHROMOSOME_NOT_FOUND' error?

ADD COMMENTlink modified 7 months ago by genomax92k • written 7 months ago by atheeth140
1

This is not a forum post, but a question.

ADD REPLYlink written 7 months ago by Carambakaracho2.2k

agreed

ADD REPLYlink written 7 months ago by lieven.sterck8.9k
1

How/where to get the WES fasta file for mus musculus?

By using sra-explorer (search for WES mouse) . Assuming by WES you are referring to whole exome sequence. You are not going to get a fasta file. You will need to get the original fastq reads and do the analysis yourself.

NCBI Datasets is the new experimental location to get large datasets like genomes.

ADD REPLYlink written 7 months ago by genomax92k

You are looking at SNP-filtered files. You are probably looking for the more general version of the genome, which is here: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/

ADD REPLYlink written 7 months ago by igor11k
0
gravatar for Carambakaracho
7 months ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:
  1. go to https://www.ncbi.nlm.nih.gov/
  2. Select genome (or assembly) and search for Mus Musculus
  3. Select genome and assembly report
  4. select the assembly of your choice, for example GRCm38 and download the assembly

As far as I know, the primary assembly is not modified with the patches, and certainly not the chromosomes added or removed

ADD COMMENTlink written 7 months ago by Carambakaracho2.2k
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