User: jaafari.omid

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Posts by jaafari.omid

<prev • 10 results • page 1 of 1 • next >
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SNP-chip Pros and Cons
... Hi all dears. I would be grateful if anyone could help me about generally advantages and disadvantages using of SNP-chips especially in GWAS! I mean how is their coverage, efficiencies and cost benefit ratio in comparison with some other methods like ddRAD and WGS? ...
snp written 4 weeks ago by jaafari.omid0 • updated 4 weeks ago by Kevin Blighe21k
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SNP Discovery Duration
... Hi Dears. I am Using Tassel3 (V1 pipeline) for GBS Analysis and Now I am in the Discovery SNPs step. I am doing this analysis with one sample because I am going to set it up. My question is how long this step (-TagsToSNPByAlignment) should take? I have allocated 20 CPUs to to run this step. It is no ...
snp written 3 months ago by jaafari.omid0 • updated 3 months ago by Kevin Blighe21k
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Comment: C: Tags to snp
... Yes, Actually I just now did it and that error was solved but another error appeared about -mUpd option. I guess if I wan to use -DiscoverySNPCallerPlugin, my command should completely change. Thanks for your helps. ...
written 3 months ago by jaafari.omid0
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Comment: C: Tags to snp
... Many thanks. But I am using the tassel 3, and the plugin name is -TagsToSNPByAlignmentPlugin for tassel3, So why it gives me that error? ...
written 3 months ago by jaafari.omid0
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Tags to snp
... Hi All Dears. This is Omid. I am using Tassel 3 (and 5). Now I am in the step entitled "TagsToSNPByAlignmentPlugin (the Discovery SNP Caller)" Unfortunately I faced with the error which says "java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -TagsToSNPByAlignmen ...
snp written 3 months ago by jaafari.omid0 • updated 3 months ago by WouterDeCoster29k
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Comment: A: GC content in DNA sequnce
... And Is it possible to guide me about Kmer? based on my information Kmer is not important for RNAseq data but I don't know how much is it important for DNA sequences like GBS. using Stacks pipeline I trimmed the raw data but after that I still have kmer content. ...
written 5 months ago by jaafari.omid0
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Comment: A: GC content in DNA sequnce
... Thanks dears for your answers to my question. ...
written 5 months ago by jaafari.omid0
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GC content in DNA sequnce
... Hello Dears. I am working on GBS data. I have trimmed my data but for some samples the FastQC showed an error related to %GC content. for example before trimming the value of GC content was 46% and after trimming it reached to %47. Actually before trimming it did not show error while its %GC content ...
genome written 5 months ago by jaafari.omid0
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(Closed) calculation of tag count
... Hello Dears. This is Omid. I am working on fish population structure using GBS data (Paired end data). I have received my data trimmed and demultiplexed from the BGI company but the data are not along with bar code information. I was going to to use tassel GBS pipeline but for the tag counting we ne ...
sequence written 5 months ago by jaafari.omid0
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Tag counting of GBS data
... Hello Dears. This is Omid. I am working on fish population structure using GBS data (Paired end data). I have received my data trimmed and demultiplexed from the BGI company but the data are not along with bar code information. I was going to to use tassel GBS pipeline but for the tag counting we ne ...
sequence written 5 months ago by jaafari.omid0

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