User: ericbrenner

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Posts by ericbrenner

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Comment: C: Ensembl ID converter not working?
... Thanks for the info! :) ...
written 2.2 years ago by ericbrenner0
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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 2.2 years ago by ericbrenner0
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Ensembl ID converter not working?
... Hi, I have some outdated Ensembl Gene IDs.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, ...
ensembl id conversion written 2.2 years ago by ericbrenner0
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Comment: C: Can you use Python to get download flanking sequences of genes from Ensembl's ol
... 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 2.2 years ago by ericbrenner0
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Can you use Python to get download flanking sequences of genes from Ensembl's older releases/assemblies?
... 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? ...
genome python sequence ensembl written 2.2 years ago by ericbrenner0 • updated 2.2 years ago by jared.andrews074.2k
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Comment: C: Is there a way to fetch genomic sequences at given coordinates without downloadi
... 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 2.2 years ago by ericbrenner0
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Is there a way to fetch genomic sequences at given coordinates without downloading fasta files?
... 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 ...
genome python sequence R dna written 2.2 years ago by ericbrenner0 • updated 2.2 years ago by Matt Shirley9.2k
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How do you use Biomart to get info about genes that didn't originate from Ensembl?
... 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 ...
genome ensembl biomart written 2.2 years ago by ericbrenner0 • updated 2.2 years ago by Jean-Karim Heriche21k
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I have DNA motifs 6-12 bp long. Trying to get conservation measurements for them.
... 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 ...
conservation motif written 2.5 years ago by ericbrenner0 • updated 2.5 years ago by shenwei3565.0k
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Comment: C: Is there anything with a poly-A tail that isn't included in Ensembl's cDNA refer
... 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 2.7 years ago by ericbrenner0

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