User: Andrew W

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Andrew W290
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Posts by Andrew W

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Comment: C: Orthologus Genes
... This might help: http://biostar.stackexchange.com/questions/15027/hello-how-we-can-convert-human-entrez-gene-ids-into-mouse-gene-ids/15031#15031 ...
written 7.4 years ago by Andrew W290
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Answer: A: Hello, How We Can Convert Human Entrez Gene Ids Into Mouse Gene Ids?
... Assuming, as neilfws suggests, that you are interested in finding orthologues, you can use NCBI's HomoloGene DB. This file (ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data) contains the mappings you need. Col2 is taxonomy ID, col3 is Entrez Gene ID. ...
written 7.5 years ago by Andrew W290
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Comment: C: Bioperl %Gc Content?
... Looks like this Q is a duplicate of http://biostar.stackexchange.com/questions/14544/help-with-counting-script ...
written 7.5 years ago by Andrew W290 • updated 6.9 years ago by Istvan Albert ♦♦ 80k
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Answer: A: Help With Counting Script
... my $na = $seq->seq; my $len = length $na; $totchrs += $len; # declare $totchrs outside your while loop my $gc = $na =~ tr/gcGC//; my $pergc = $gc/ $len * 100; $pergc = sprintf "%3.2f", $per_gc; # if you want it formatted Or you can look at this script: https:/ ...
written 7.5 years ago by Andrew W290 • updated 6.9 years ago by Istvan Albert ♦♦ 80k
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Comment: C: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
... Ensembl has more genes than RefSeq (at least for human), which might partly explain why you only get mappings for 3/4 of your genes. ...
written 7.5 years ago by Andrew W290
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Answer: A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
... Looking just at the mapping of Ensembl gene IDs to NCBI Gene IDs (or locus names- I would work with Gene IDs first and convert them to locus names at the end of the processing), you can use CCDS flatfiles (in ftp://ftp.ncbi.nih.gov/pub/CCDS/current_human/) and Ensembl cDNA Fasta files (e.g. ftp://ft ...
written 7.5 years ago by Andrew W290
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Comment: C: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... Ok, thanks, I understand now. Sorry, I should have been more precise in the original post. It's a good idea and perhaps I will find a way to use it, or at least someone with longer reads who sees this entry can give it a try. ...
written 7.5 years ago by Andrew W290
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Comment: C: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... "and so the flanking data (outside the miR) could be used to assign the read to a putative location on the genome of the near relative" I'm sorry, I'm still a bit confused. I don't understand whence I am getting this flanking sequence. I have short reads (most ~22 bps) from my RNA deep sequencing ...
written 7.5 years ago by Andrew W290
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Comment: C: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... "I would have hoped miRBase would find." That should read "I would have hoped miRDeep would find." ...
written 7.5 years ago by Andrew W290
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Comment: C: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... (cont...) results, I'm not sure. Before I try it again, though, I will test the miRBase entries to see how easy they are to pair together. Maybe it's a problem even with miRNAs, even with clean data. ...
written 7.5 years ago by Andrew W290

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