Hi everyone!
I have been trying all day long to download coordinates for several refseqs that are mRNA and non-coding RNAs and been failing getting few or none results. So How one could retrieve locations using UCSC table browser or MySQL query for example for the following RefSeqs?
NM_001080438
XM_001717469
XR_040005
XR_040875
XM_001134462
NR_002823
XM_940966
XM_942664
XR_015764
NM_024018
XR_017648
NM_017609
NM_182901
XR_041798
Sorry for this newbie question but I'm totally lost with this
Any kind of hel would be really appreciated!!
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written
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daniel.soronellas
the ucsc doesn't use all the accession numbers:
http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg19&position=XR_041798
Sorry, couldn't locate XR_041798 in genome database
probably because this record has been listed as deprecated in genbank;
http://www.ncbi.nlm.nih.gov/nuccore/XR_041798
record removed. This record was removed as a result of standard genome annotation processing. See the genome build documentation at http://www.ncbi.nlm.nih.gov/genome/guide/build.html for further information, or contact info@ncbi.nlm.nih.gov.
you can always blat your sequences on the human genome.
Thanks for your answer!
I think I will have to use BLAT, do you know if requires the RefSeq or FASTA sequences? Because I've tried with all my RefSeqs and gives me an error
Just to know If I'm in the right way.
Many Thanks!
this should be a comment, not an answer. RefSeq is a database, fasta is a sequence format. blat uses FASTA.
Thanks for your post and suggestion
Do you how I could get the FASTA seqs for a bunch of RefSeqs?
Thanks.
use the NCBI e-utilities , search biostar for many examples.
If you good with command line download refseq gene list from UCSC and you can use join command to join the accession ids otherwise follow these steps ..
and done!
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