User: diviya.smith

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diviya.smith50
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United States
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4 years, 11 months ago
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Posts by diviya.smith

<prev • 22 results • page 1 of 3 • next >
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Computing pairwise sequence divergence
... I need to compute pairwise sequence divergence between two species. I have the fasta files of the two sequences aligned to an outgroup. I was wondering if you can suggest a program for doing this. It is important if the method is able to handle missing data - aka ignore missing data. I can comfortab ...
fasta multiple sequence divergence written 5.8 years ago by diviya.smith50
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Comment: C: Convert cM/MB to cM
... Actually figured it out -was just looking at the wrong numbers before. To col 3 = (pos - prevpos)* cM/MB. Not sure how to close/ delete this post though. ...
written 5.9 years ago by diviya.smith50
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Convert cM/MB to cM
... I have a naive question about recombination maps. I need to use the genetic position in cM but I only have the physical position and rate in cM/MB. How do I convert this to a position in cM? I looked at the HapMap recombination maps and the conversion is not directly obvious to me.  Chromosome    P ...
humans recombination map written 5.9 years ago by diviya.smith50
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Comment: C: Getting A Vcf File From A Fasta Alignment
... Thanks! This is very helpful. ...
written 6.0 years ago by diviya.smith50
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Comment: C: Getting A Vcf File From A Fasta Alignment
... Hi Pierre, I am looking for a program for converting fasta -> vcf and I found this discussion and your code very helpful. However, I have a couple of questions regarding this output -  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Ind1 Ind2 Ind3 chrUn 6 . G C . . ...
written 6.0 years ago by diviya.smith50
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Comment: C: liftover a fasta file
... Thanks for the suggestion. I tried BLAT but I think it has a max sequence limit on the online version - perhaps that can be changed for running it locally. Is there any other option? BLAT is not applicable for my analysis as I want to remap the coordinates of the ancestral sequence and so I dont rea ...
written 6.0 years ago by diviya.smith50
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Comment: C: Converting bam -> fasta
... Thanks but bam -> fa generates an output for each read pair - I want to generate a combined consensus bam file.  Any suggestions?   ...
written 6.1 years ago by diviya.smith50
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Converting bam -> fasta
... I was wondering if there is an good way of converting an aligned bam into a consensus fasta file. I was following the solution on https://www.biostars.org/p/65885/  but the discuss has me a little worried. In addition, the first step takes a long time and my runs keep failing without any errors. Any ...
alignment sequencing written 6.1 years ago by diviya.smith50 • updated 5.2 years ago by Biostar ♦♦ 20
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liftover a fasta file
... I was wondering if there is an easy way to liftover an entire genome. I want to liftover a fasta file from pantro2 to pantro4 genome positions. There was no ancestral sequence generated for pantro4. Is there an easy way to do this? I think the UCSC liftover will be extremely slow for regions. Dont w ...
assembly sequence written 6.1 years ago by diviya.smith50
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Comment: C: Access Hash With 250M Entries
... I am giving the problem 10GB of memory and it still runs out of memory. I am currently doing something very simple - while (my $line = ) { #read line and store in array } However, I think the db solution would be much better. I am looking into Berkeley db instead. Not sure if that the best soluti ...
written 6.8 years ago by diviya.smith50

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