User: andrey.v.shubin

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Posts by andrey.v.shubin

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Calculate RNAseq coverage of a transcript
... Thanks to WouterDeCoster and Bastien Herve for their answers! I have found out that bedtools does exactly what I need: bedtools coverage -hist -abam "your bam file" -b "your bed file" > "file with results" ...
written 4 days ago by andrey.v.shubin50
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Calculate RNAseq coverage of a transcript
... Hi Biostars community, I have bam files with RNA-seq results from ~1000 of single cell samples. For every transcript in each sample, I would like to calculate what percentage of spliced transcript's length is covered by aligned reads. Besides, It would be great to have this value for coding part of ...
rna-seq transcriptome written 7 days ago by andrey.v.shubin50
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Finding more information about a homozygote of interest
... Hello, I am interested in the mutation 3:113303616 G / T in SIDT1 gene. According to ExAC database, there is only one homozygotic variant detected so far, and this person is from East Asia - this is the only information given there (http://exac.broadinstitute.org/variant/3-113303616-G-T). Are the ...
snp written 5 months ago by andrey.v.shubin50
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Comment: C: Finding homozygotes with SNP of interest
... Thank you, I have found exactly what I need. ...
written 6 months ago by andrey.v.shubin50
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Finding homozygotes with SNP of interest
... Hello, I am a very new person in genetic variation analysis, so my question may be very simple. I am interested in the SNP rs764867354 in SidT2 gene that leads to loss of a start codon. (http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000149577;r=11:117178733-117197445;v=rs76 ...
ensembl homozygote snp written 6 months ago by andrey.v.shubin50 • updated 6 months ago by Emily_Ensembl14k
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Finding a downstream ORF
... Hi everyone, I have a list of several hundreds of bacterial protein identifiers (e.g., WP_040242412.1), and I need to find which ORF follows downstream. Using Entrez Direct I can get genome identifiers, coordinates and strand orientation for ORFs for these proteins (e.g., WP_040242412.1: NZ_CDGZ010 ...
entrez direct orf genome written 12 months ago by andrey.v.shubin50 • updated 12 months ago by EVR450
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Answer: A: from GI or protein ID to genome coordinates
... I have inquired NCBI support service about this question. This is their answer: The information is stored in the identical protein report. https://www.ncbi.nlm.nih.gov/protein/WP_012146310.1?report=ipg The following is an example of multiple wp accession input, combined with grep to retrieve only ...
written 13 months ago by andrey.v.shubin50 • updated 13 months ago by genomax39k
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from GI or protein ID to genome coordinates
... Hi! I have a list of protein blast hits in RefSeq ID format (e.g., WP_012146310.1) , and now I want to retrieve genome coordinates of genes encoding these proteins. I am using Entrez Direct to cope with it. Having the RefSeq ID, I got gi (501096268) and genome accession number (NC_009832.1), but I ...
entrez direct gi genome coordinates refseq written 13 months ago by andrey.v.shubin50 • updated 6 months ago by cmdcolin690

Latest awards to andrey.v.shubin

Scholar 4 days ago, created an answer that has been accepted. For A: from GI or protein ID to genome coordinates
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: from GI or protein ID to genome coordinates
Scholar 13 months ago, created an answer that has been accepted. For A: from GI or protein ID to genome coordinates

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