User: Denis

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Denis140
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Posts by Denis

<prev • 85 results • page 1 of 9 • next >
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The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
... I've installed `sratoolkit.2.10.0` at my home on a cluster. I have to download a numerous `SRR` accessions to my home directory. There are a several options, as i can understand: 1. `fastq-dump` 2. run `prefetch`utility, then convert resulted `sra` files to `fastq` by `fastq-dump` 3. `faster ...
genome sequence written 6 days ago by Denis140
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Comment: C: Can I combine the GBS data with Whole Genome Resequencing for GWAS analysis
... Hi! Did you manage the issue? ...
written 11 weeks ago by Denis140
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Frontmost snp callers for plant genomes
... Hello! I'm working with `WGS` data and looking for the most used software to find high quality `SNPs` and `INDELs` in plants with different ploidy levels. I've found two related posts, but seems they both already not up to date and futhermore not focused on plant genomes: https://www.biostars.org/p ...
genome alignment next-gen snp written 11 weeks ago by Denis140 • updated 11 weeks ago by JC9.3k
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Comment: C: Making nice plots based on the different metrics from VCF file
... It looks promising. Defenitely worth to try. ...
written 3 months ago by Denis140
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Comment: C: Methods for Doing Consensus Variant Calling between multiple callers
... Hi! Have you used ATpoint's solution? ...
written 4 months ago by Denis140
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Forum: Using Graphics Processing Units (GPUs) in bioinformatics
... In our days GPUs have installed on many HPC clusters. I'm using HPC cluster for de novo assembly, SNP calling, reads mapping and other bioinformatic routines. I'm wondering for which bioinformatic tasks/algorithms i may apply GPUs? How can i benefit from using GPUs in my computations? ...
forum gpu algorithm written 4 months ago by Denis140 • updated 7 weeks ago by RochMesa20
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Comment: C: Good questions and answers resources (forums) on Ecology and Statistics
... Thank you again! I'll try these. ...
written 5 months ago by Denis140
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Comment: C: Good questions and answers resources (forums) on Ecology and Statistics
... Thanks! There are some techniques/approaches which are in use basically in ecology now and poorly known among statisticians,but require strong statistical background. I think that's the main issue in my case. ...
written 5 months ago by Denis140
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Good questions and answers resources (forums) on Ecology and Statistics
... Hi there! I'm looking for a good place for asking questions related to Ecology and Statistics. I've tried `Cross Validated`, but still didn't get any answers on my posts. Thanks! ...
ecology written 5 months ago by Denis140 • updated 5 months ago by The160
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Understanding of fields meaning in HapMap.hmc.txt file from UNEAK pipeline in Tassel 3.0
... Where can i find description for all fields in `HapMap.hmc.txt` file i got in `UNEAK` pipeline? I need that to calculate `depth of coverage (DP)` and `allele depth (AD)` to use these for `VCF` file filtration. Is there any plugin in `Tassel` to filter out variants in resulted `VCF` file based on `DP ...
genome snp sequencing written 5 months ago by Denis140

Latest awards to Denis

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Voter 5 weeks ago, voted more than 100 times.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Popular Question 4 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Scholar 6 months ago, created an answer that has been accepted. For A: Bootstrap values on the phylogenetic tree in Ape r package
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bootstrap values on the phylogenetic tree in Ape r package
Popular Question 7 months ago, created a question with more than 1,000 views. For Demultiplexing of the Illumina PE data
Supporter 18 months ago, voted at least 25 times.

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