User: ggman

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ggman70
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Posts by ggman

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Tools to calculate binned Dxy?
... I think those are only for Fst and Pi, unless if I am misreading them. ...
written 23 days ago by ggman70
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optical mapping companies in the USA
... Greetings, What are your experiences with optical mapping the US? I found a reputable company in BioNano but are there any other options that are of the same caliber? GG ...
optical mapping genomes assembly written 23 days ago by ggman70 • updated 23 days ago by RamRS18k
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Comment: C: Tools to calculate binned Dxy?
... Right, those take calculate it per site as opposed to fixed windows. ...
written 23 days ago by ggman70
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Comment: C: Tools to calculate binned Dxy?
... Yes, fixed-window sizes. ...
written 23 days ago by ggman70
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Comment: C: Tools to calculate binned Dxy?
... Thanks, much appreciated! ...
written 24 days ago by ggman70
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Tools to calculate binned Dxy?
... Hi all, Are there any tools that can calculate binned Dxy? I have found some that are capable of calculating per site Dxy, such as ANGSD. Any suggestions would be appreciated. An offshoot of this question - what's the best way to stay informed about latest developments in genomic analysis tools? ...
genome R dxy snp written 24 days ago by ggman70
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Creating bins based on scaffold size file
... Greetings all, I am attempting to create bins/windows based on a genome file which contains data like the one below. I was wondering if anyone has encountered a program that can create windows for you based on intervals such as 100k, 10k, 50k.. etc. While I can simply manipulate VCFtools PI output ...
assembly bin sequence snp alignment written 6 weeks ago by ggman70 • updated 6 weeks ago by Pierre Lindenbaum112k
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... Hello Ronald, I have a question about what you are saying. So for the average coverage you are stating, that would be per scafffold correct? I attempted to open a topic recently and was referred to this one :) Cheers ...
written 8 weeks ago by ggman70
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(Closed) Obtaining coverage of genome from Bam Files
... Greetings friends, I am attempting to obtain how much coverage my bam files have relative to my reference genome. I was wondering what kind of tools were available for this? I thought samtools would have some kind of function built in for this kind of task but I can't seem to find one. Any suggesti ...
genome bam samtools snp sequencing written 9 weeks ago by ggman70
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Running ANGSD using multiple -doMaf options at once
... Hello friends, I am attempting to obtain a csv file running angsd with the following data chromo position major minor ref knownEM unknownEM nInd When I run angsd using the command below, it appears to be ignoring -doMaf 2 and only outputting my results as if it only ran -doMaf 1 ...
domaf next-gen angsd snp written 10 weeks ago by ggman70 • updated 20 days ago by Biostar ♦♦ 20

Latest awards to ggman

Popular Question 6 weeks ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data
Student 8 weeks ago, asked a question with at least 3 up-votes. For samtools sorting and indexing
Epic Question 5 months ago, created a question with more than 10,000 views. For samtools sorting and indexing
Great Question 14 months ago, created a question with more than 5,000 views. For samtools sorting and indexing
Popular Question 14 months ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data
Popular Question 3.1 years ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data

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