User: greentailedmouse

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Posts by greentailedmouse

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Which tools do you miss?
... A replacement for AAT and/or exonerate. Some parts of eukaryotic annotation pipelines are older than a decade and not developed or maintained. ...
written 6 months ago by greentailedmouse50
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Comment: C: Tool to generate a chain file from an agp file
... No, I gave up on it. Sorry! ...
written 3.8 years ago by greentailedmouse50
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Tool to generate a chain file from an agp file
... Hi all, here is some background to my question in the title: I have two genome versions, a scaffolded and unscaffolded one; as luck has it, the annotated version is the unscaffolded one. I would like to update the coordinates in the GFF file to the scaffolded version. I wanted to use crossMap (http ...
agp crossmap gff chain written 4.2 years ago by greentailedmouse50 • updated 3.3 years ago by Malcolm.Cook1.2k
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Comment: C: Get upstream and downstream intergenic regions in R
... I'll mark your answer as accepted since I've done something similar in the end; but it also answers my original question - namely, there is no such function or parameter in Granges. Thanks! ...
written 4.3 years ago by greentailedmouse50
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Get upstream and downstream intergenic regions in R
... Hi all, I would like to get the upstream and downstream intergenic distance between two genes in R (taking into account that some genes may overlap). For example - in the following case I would expect to get a the upstream distance of 5 for gene A, a distance 0 or negative for downstream of A, and ...
R granges intergenic written 4.4 years ago by greentailedmouse50 • updated 4.4 years ago by ddiez1.9k
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Haplotype resolving (phasing) from BAM file
... Hi all, I have a question about what I first thought would be a trivial task. I would like to resolve the haplotypes of a non-model (diploid) species. I have a genome assembly, and a bam file where the reads (that were used for genome assembly) are mapped. The genotype of the mapped reads is thus t ...
haplotype bam written 4.4 years ago by greentailedmouse50
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Comment: C: Bio::Searchio For Hmmer3 Output (Best Domain E-Value And I-Evalue)
... Thanks! In the end I did write my own script; I would prefer to use the perl package for the sake of code consistency. ...
written 7.0 years ago by greentailedmouse50
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Bio::Searchio For Hmmer3 Output (Best Domain E-Value And I-Evalue)
... I'm using Bio::SearchIO to parse HMMER3 output. I am able get the significance of each sequence (which is located in the table on top of the output) with $hit->significance. I can also get the c-Evalue by using $hsp->significance. However, the more informative number would be the i-Evalue (fr ...
bioperl hmmer written 7.0 years ago by greentailedmouse50 • updated 4.6 years ago by Biostar ♦♦ 20

Latest awards to greentailedmouse

Popular Question 3.8 years ago, created a question with more than 1,000 views. For Tool to generate a chain file from an agp file
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Bio::Searchio For Hmmer3 Output (Best Domain E-Value And I-Evalue)
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Get upstream and downstream intergenic regions in R
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Bio::Searchio For Hmmer3 Output (Best Domain E-Value And I-Evalue)

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