User: ggman

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ggman70
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Posts by ggman

<prev • 36 results • page 1 of 4 • next >
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Comment: C: BWA-MEM Syntax Understanding
... Gotcha, thanks Devon! ...
written 7 weeks ago by ggman70
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BWA-MEM Syntax Understanding
... Hey all, I am trying to switch over from bowtie to BWA. There are many options that I don't understand once you attempt to align reads to the reference genome. Would it be better to leave these options as default, especially when it comes to the scoring? GG ...
bwa-mem alignment written 7 weeks ago by ggman70 • updated 7 weeks ago by Devon Ryan86k
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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 12 weeks 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 12 weeks ago by ggman70 • updated 12 weeks ago by RamRS19k
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Comment: C: Tools to calculate binned Dxy?
... Right, those take calculate it per site as opposed to fixed windows. ...
written 12 weeks ago by ggman70
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Comment: C: Tools to calculate binned Dxy?
... Yes, fixed-window sizes. ...
written 12 weeks ago by ggman70
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Comment: C: Tools to calculate binned Dxy?
... Thanks, much appreciated! ...
written 12 weeks 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 12 weeks 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 3 months ago by ggman70 • updated 3 months ago by Pierre Lindenbaum115k
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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 4 months ago by ggman70

Latest awards to ggman

Popular Question 3 months ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data
Student 4 months ago, asked a question with at least 3 up-votes. For samtools sorting and indexing
Epic Question 8 months ago, created a question with more than 10,000 views. For samtools sorting and indexing
Great Question 16 months ago, created a question with more than 5,000 views. For samtools sorting and indexing
Popular Question 16 months ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For GC percent script; reading a fasta formatted data

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