Question: How to get the chromosome numbers from RefSeq accession IDs?
0
gravatar for birdguy.saikat
3.8 years ago by
birdguy.saikat10 wrote:

I have an array of RefSeq accession IDs, which looks like the following:

NC_000001.11 NC_000002.12 NC_000003.12 NC_000004.12 NC_000005.10 NC_000006.12 NC_000007.14 NC_000008.11 NC_000009.12 NC_000010.11 NC_000011.10 . . .

I am interested in knowing which chromosomes they refer to? Is there a way to automatically retrieve this information?

refseq • 2.4k views
ADD COMMENTlink modified 8 months ago by vkkodali2.0k • written 3.8 years ago by birdguy.saikat10

Definately not a good solution but you can upload the ids to batch entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez) and get the summary as output text file which gives the chromosome name.

ADD REPLYlink written 3.8 years ago by microfuge1.7k

See my comment on your previous question CGAT: Error while running gtf2gtf

ADD REPLYlink written 3.8 years ago by i.sudbery8.2k
1
gravatar for Devon Ryan
3.8 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

It's not ideal, but you can download the assembly report, which has these IDs and the associated chromosome names (in UCSC and Ensembl nomenclatures). I have to do this sort of thing when I update the chromosome name conversion tables :(

ADD COMMENTlink written 3.8 years ago by Devon Ryan95k
0
gravatar for srijan.verma44
12 months ago by
srijan.verma440 wrote:

You could find the chromosomes of the alternative accession numbers (NT_... / NW_...) in this directory.
Download the files with the name :
1. alts_accessions_GRCh38.p12
2. chr_NC_gi
3. chr_accessions_GRCh38.p12
4. unplaced_accessions_GRCh38.p12
5. unlocalized_accessions_GRCh38.p12

Once you download them, you might be prompted to enter some 'Keychain Access' password. The workaround which I found for this is that to convert the downloaded file to a '.txt' format and you'll be able to view whats inside the file.

An extract from the file is given below :

Chromosome RefSeq Accession.version

1 NW_012132914.1
1 NW_015495298.1
9 NW_009646201.1
10 NW_011332692.1
11 NW_015148966.1
Reference : This article.

ADD COMMENTlink modified 12 months ago • written 12 months ago by srijan.verma440
0
gravatar for vkkodali
8 months ago by
vkkodali2.0k
United States
vkkodali2.0k wrote:

See this post: A: How to obtain the chromosome out of an accession number? In short, NCBI RefSeq provides assembly_report.txt files with each genome assembly that has the mapping information in a tab-delimited table. That would be the most up-to-date source for this sort of information.

ADD COMMENTlink written 8 months ago by vkkodali2.0k
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