User: andrey.v.shubin
andrey.v.shubin • 60
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Posts by andrey.v.shubin
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... 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 2.7 years ago by
andrey.v.shubin • 60
6
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5 follow
1
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... 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 ...
written 2.7 years ago by
andrey.v.shubin • 60
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... 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 ...
written 3.1 years ago by
andrey.v.shubin • 60
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2
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716
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2
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... Thank you, I have found exactly what I need. ...
written 3.2 years ago by
andrey.v.shubin • 60
5
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2
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716
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2
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... 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 ...
written 3.2 years ago by
andrey.v.shubin • 60
• updated
3.2 years ago by
Emily_Ensembl ♦ 21k
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... 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 ...
written 3.7 years ago by
andrey.v.shubin • 60
• updated
3.7 years ago by
EVR • 570
5
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2.0k
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4
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... 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 3.8 years ago by
andrey.v.shubin • 60
• updated
3.8 years ago by
genomax ♦ 87k
7
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4
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... 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 ...
written 3.8 years ago by
andrey.v.shubin • 60
• updated
3.2 years ago by
cmdcolin • 1.4k
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Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For from GI or protein ID to genome coordinates
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2.7 years ago,
created an answer that has been accepted.
For A: from GI or protein ID to genome coordinates
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: from GI or protein ID to genome coordinates
Scholar
3.8 years ago,
created an answer that has been accepted.
For A: from GI or protein ID to genome coordinates
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