User: ypriverol

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ypriverol0
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Posts by ypriverol

<prev • 12 results • page 1 of 2 • next >
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Answer: A: rna seq docker
... You can search for containers in bioinformatics in www.biocontainers.pro/registry or request for them in github.com/BioContainers ...
written 6 days ago by ypriverol0
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Comment: C: Assembly Id to UCSC names
... Green mark in the post ? Where? ...
written 6 days ago by ypriverol0
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Assembly Id to UCSC names
... Hi all: Another NCBI/UCSC question. I have all the assembly Ids such as: GCA_000001405.15 GCA_000164845.2 And I would like to get the corresponding UCSC assembly name: hg38 vicpac2 If the Assembly ID corresponds to a patch, and not UCSC is available for it, then I would like to have the cl ...
ncbi ensembl ucsc written 6 days ago by ypriverol0
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Comment: A: chrom.sizes computed locally
... Do you know how to do it from the fasta files ensembl provides here: https://m.ensembl.org/info/data/ftp/index.html ...
written 8 days ago by ypriverol0
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Comment: C: chrom.sizes computed locally
... The problem is that known of the APIs said on which files these numbers are compute. ...
written 8 days ago by ypriverol0
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Comment: C: chrom.sizes computed locally
... I would like to do it based on the fasta files they provide in the FTP. ...
written 8 days ago by ypriverol0
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chrom.sizes computed locally
... Hi all: In order to be able to convert from bed files to bigbed using the UCSC tool (bedToBigBed) `chrom.sizes` is needed. How can this number be computed without querying the UCSC and ENSEMBL APIs?. ...
bigbed bed ucsc ensembl written 8 days ago by ypriverol0 • updated 6 days ago by cpad01121.9k
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Comment: C: Retrieve all ids from NCBI
... Thanks for your quick response. ...
written 10 days ago by ypriverol0
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Comment: C: Retrieve all ids from NCBI
... This is strange: Your results are: 10454 My results with the url are: 246934 (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=bioproject&term=all%5Bfilter%5D&retmax=999999) The results in their browser are: 228784 (https://www.ncbi.nlm.nih.gov/bioproject/browse/) ...
written 10 days ago by ypriverol0
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Comment: C: Retrieve all ids from NCBI
... Hi @genomax thanks for your quick answer. Do you know a way to do it programmatically. I found this one https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=bioproject&term=all%5Bfilter%5D&retmax=999999 but I don't know if is the best one. Regards Yasset ...
written 10 days ago by ypriverol0

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