User: ericbrenner
ericbrenner • 0
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Posts by ericbrenner
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C: Ensembl ID converter not working?
... Thanks for the info! :) ...
written 3.2 years ago by
ericbrenner • 0
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Comment:
C: Ensembl ID converter not working?
... The ID History Converter tool on Ensembl's webite: http://www.ensembl.org/Homo_sapiens/Tools/IDMapper?db=core
Do you have a different one you'd recommend? ...
written 3.2 years ago by
ericbrenner • 0
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... Hi, I have some outdated Ensembl Gene IDs. I tried using Ensembl's ID converter tool to get the new versions of the IDs but it just spits back the same ID to me that wasn't working in the first place. For example, with "ENSGALG00000015646", the tool says that the ID is still in the current release, ...
written 3.2 years ago by
ericbrenner • 0
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... I just got it sort of working with Ensembl's REST API, but I have a couple thousand of genes, and it has a max size of 50 per post request :( ...
written 3.2 years ago by
ericbrenner • 0
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... I have some Ensembl ID's from an older assembly of the chicken genome, and I'm trying to get the promoter sequences for them. Is there a way to pull the sequences from Ensembl in Python with Biomart or something? ...
written 3.2 years ago by
ericbrenner • 0
• updated
3.2 years ago by
jared.andrews07 ♦ 7.9k
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... Does "GET sequence" on the REST API work for previous assemblies/releases of other species? I only know how to do it for grch37, but is that it. Thanks :) ...
written 3.2 years ago by
ericbrenner • 0
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... So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the genome as a fasta file and then use pyfaidx to extract the sequences at the given positions. But no ...
written 3.2 years ago by
ericbrenner • 0
• updated
3.2 years ago by
Matt Shirley ♦ 9.4k
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... Hi,
I've really liked using Biomart in the past, but I've recently realized that I don't know how to use it to get info on genes like this:
http://www.ensembl.org/Gallus_gallus/Gene/Summary?db=otherfeatures;g=416764;r=15:25280-34065;t=XM_415059.5
which don't originate from Ensembl and don't have a ...
written 3.2 years ago by
ericbrenner • 0
• updated
3.2 years ago by
Jean-Karim Heriche ♦ 23k
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... I have about 200 short nucleotide motifs (6-12 bp in length) from the human genome, and I'm trying to see how conserved they are across vertebrates. I was thinking that I'd need to make a bed file for each motif that lists all of its occurrences in the human genome. From there, I could map the beds ...
written 3.5 years ago by
ericbrenner • 0
• updated
3.5 years ago by
shenwei356 ♦ 5.6k
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... I was thinking things like lncRNA's or miRNA intermediates that haven't finished being processed. I've since learned that miRNA's are not included. Not sure about the rest. Basically, if I have raw RNA-seq data (corresponding to everything with a polyA tail), what reference(s) should I use for annot ...
written 3.7 years ago by
ericbrenner • 0
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