User: Denis

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Denis190
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Posts by Denis

<prev • 99 results • page 2 of 10 • next >
6
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1
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472
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Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading
... Hi, I've executed the `prefetch` command of `SRA toolkit` which is in my case supposed to call the `Aspera ascp` command line utility internally. My command line was: /home/sratoolkit.2.10.0-ubuntu64/bin/prefetch -a "/home/.aspera/connect/bin/ascp|/home/.aspera/connect/etc/asperaweb_id_dsa.openssh ...
genome next-gen written 3 months ago by Denis190
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168
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Comment: C: Freebayes variant calling understanding
... Try to check this position in different samples, perhaps you'll find several alternative alleles for that position. ...
written 4 months ago by Denis190
1
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Comment: C: Freebayes variant calling understanding
... In some loci you have more than just two alleles and for those loci the caller use notations like 2,3, etc. This variants are multiallelic and were filtered out when you tried to leave only biallelic ones. ...
written 4 months ago by Denis190
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4
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2.2k
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4
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Comment: C: Extract SNPs flanking sequences based on VCF and genome Fasta files
... Hi, It seems that you have to add additional block with `if` statement to check if `record.pos-1-flank` is greater than 0. Perhaps the same aproach and for `record.pos-1+len(record.ref)+flank` it should be smaler or at least equal than chromosome length. But i'm not sure as i din't run it. ...
written 5 months ago by Denis190
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273
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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 5 months ago by Denis190
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642
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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 8 months ago by Denis190
2
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1
answer
159
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1
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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 8 months ago by Denis190 • updated 8 months ago by JC10k
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3
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1.3k
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3
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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 8 months ago by Denis190
1
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1
answer
483
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1
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Comment: C: Methods for Doing Consensus Variant Calling between multiple callers
... Hi! Have you used ATpoint's solution? ...
written 10 months ago by Denis190
9
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4
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744
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5 follow
4
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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 10 months ago by Denis190 • updated 7 months ago by RochMesa20

Latest awards to Denis

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Canonical Correspondence Analysis in R with Vegan library
Centurion 6 weeks ago, created 100 posts.
Popular Question 3 months 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 3 months ago, created a question with more than 1,000 views. For Extract SNPs flanking sequences based on VCF and genome Fasta files
Popular Question 5 months 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 6 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Voter 7 months ago, voted more than 100 times.
Popular Question 8 months 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 10 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 12 months ago, created an answer that has been accepted. For A: Bootstrap values on the phylogenetic tree in Ape r package
Teacher 12 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 13 months ago, created a question with more than 1,000 views. For Demultiplexing of the Illumina PE data
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