User: greentailedmouse
greentailedmouse • 40
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Posts by greentailedmouse
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... No, I gave up on it. Sorry! ...
written 19 months ago by
greentailedmouse • 40
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7 follow
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... 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 ...
written 2.0 years ago by
greentailedmouse • 40
• updated
13 months ago by
Malcolm.Cook • 900
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... 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 2.1 years ago by
greentailedmouse • 40
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... 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 ...
written 2.1 years ago by
greentailedmouse • 40
• updated
2.1 years ago by
ddiez • 1.7k
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... 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 ...
written 2.2 years ago by
greentailedmouse • 40
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... 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 4.8 years ago by
greentailedmouse • 40
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... 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 ...
written 4.8 years ago by
greentailedmouse • 40
• updated
2.4 years ago by
Biostar ♦♦ 20
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2.0 years ago,
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For Bio::Searchio For Hmmer3 Output (Best Domain E-Value And I-Evalue)
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