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105 results • Page
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Filtering for tag:
parallel
•
reset
0
votes
0
replies
6
views
Parallel haplotyping
gVCF
GATK
HaplotypeCaller
merge
parallel
1 hour ago by
Poshi
• 0
0
votes
2
replies
107
views
Issues downloading fastq data
fastq-dump
parallel
SRA
5 days ago by
pablojosegiraudi
• 0
1
vote
6
replies
228
views
Using GNU parallel to speed up merging VCFs with bcftools
vcf
parallel
gwas
bcftools
bash
8 weeks ago by
mfshiller
▴ 10
1
vote
3
replies
146
views
Trim_galore with gnu parallel
parallel
trim_galore
RNA-Seq
trim
fastq
9 weeks ago by
francesca3
▴ 40
14
votes
15
replies
263
views
Is it possible to run haplotypecaller in gnu parallel ?
gnu parallel
HaplotypeCaller
parallel
gatk
11 weeks ago by
dare_devil
★ 1.4k
1
vote
2
replies
155
views
fastq processing with parallel command
parallel
bioinformatics
fastq
gatk
updated 3 months ago by
ATpoint
47k • written 3 months ago by
SurdanBurasi
• 0
1
vote
9
replies
673
views
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 3 months ago by
chenyangkang24
• 0 • written 3 months ago by
whb
▴ 10
341
votes
80
replies
123k
views
32 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools
parallel
next-gen
ngs
Tool
4 months ago by
ole.tange
★ 4.0k
0
votes
2
replies
178
views
Using Parallel GNU
parallel
unix
trimming
updated 4 months ago by
Ram
32k • written 4 months ago by
whb
▴ 10
0
votes
4
replies
202
views
Best way to find intervals for parallelization of joint variant calling
variants
parallel
updated 4 months ago by
Pierre Lindenbaum
135k • written 4 months ago by
William
★ 4.8k
0
votes
3
replies
268
views
Using GNU Parallel to read arguments into a bash script
gnu
parallel
bash
6 months ago by
SaltedPork
▴ 110
0
votes
1
reply
203
views
Can dmn {DirichletMultinomial} be run on multiple cpu cores in R?
R
multi-core
Dirichelet
microbiome
parallel
7 months ago by
mschmidt
▴ 50
8
votes
5
replies
605
views
GNU parallel command with several multiple arguments
parallel
gnu parallel
updated 8 months ago by
ole.tange
★ 4.0k • written 8 months ago by
FGV
▴ 120
1
vote
6
replies
294
views
Parallelization in R 2020
R
parallel
BiocParallel
doParallel
snowfall
updated 10 months ago by
zx8754
10k • written 10 months ago by
Konstantinos Yeles
▴ 110
6
votes
4
replies
669
views
GNU Parallel Number of Possible Threads
RNA-Seq
STAR
GNU
Parallel
multithreading
updated 11 months ago by
ATpoint
47k • written 11 months ago by
nickhir
▴ 30
7
votes
9
replies
281
views
Time ran out in SLURM operation
SLURM
software error
parallel
multithreading
11 months ago by
guardsquirrel
• 0
8
votes
5
replies
1.6k
views
How to parallelize bcftools mpileup with GNU parallel?
bcftools
mpileup
parallel
14 months ago by
beausoleilmo
▴ 370
0
votes
3
replies
648
views
How to run 2 programme one after another using single SLURM?
SLURM
parallel
updated 15 months ago by
Mensur Dlakic
★ 10k • written 15 months ago by
kabir.deb0353
▴ 20
7
votes
3
replies
979
views
mclapply on AWS
R
CRAN
parallel
mclapply
AWS
20 months ago by
joe
▴ 180
5
votes
8
replies
944
views
using GNU parallel for bwa mem and samtools
samtools
bwa
parallel
updated 20 months ago by
ole.tange
★ 4.0k • written 20 months ago by
little_more
▴ 40
3
votes
3
replies
786
views
Getting error with awk when using parallel processing in bedtools
bedtools
intersect
parallel
updated 21 months ago by
ATpoint
47k • written 21 months ago by
nastaran.esfahani
▴ 10
1
vote
6
replies
603
views
Speed up psiblast of 11k alignments
psiblast
parallel
updated 21 months ago by
Biostar
20 • written 23 months ago by
fhsantanna
▴ 520
2
votes
5
replies
2.1k
views
How about my parallel bwa+gatk pipeline?
gatk
parallel
pipeline
ngs
updated 22 months ago by
Charles Warden
8.0k • written 3.4 years ago by
bluemonster0808
▴ 40
0
votes
1
reply
427
views
RepeatModeler contig size filter and parallelization
RepeatModeler
Contig length
Parallel
2.1 years ago by
Anand Rao
▴ 350
3
votes
4
replies
1.6k
views
Parallel for bwa mem - problem with -R argument for ID and SM
parallel
alignment
bwa
updated 2.1 years ago by
ATpoint
47k • written 3.1 years ago by
Korsocius
▴ 180
1
vote
7
replies
868
views
Snowfall Parallelisation to compute Correlation Matrix
snowfall
parallel
2.1 years ago by
pablo
▴ 160
5
votes
3
replies
1.7k
views
Best approach for parallelizing bwa mem over multiple CPUs
bwa
hpc
parallel
updated 2.2 years ago by
GenoMax
99k • written 2.2 years ago by
olikidrod
• 0
7
votes
10
replies
2.8k
views
6 follow
trying to use gnu parallel and blast
blast
parallel
gnu parallel
blastx
optimization
updated 2.4 years ago by
Giuseppe
• 0 • written 3.8 years ago by
pablo61991
▴ 90
2
votes
2
replies
3.2k
views
GATK: -nct and -nt
gatk
parallel
updated 2.4 years ago by
nick.carleson
▴ 10 • written 4.0 years ago by
fire_water
▴ 80
12
votes
0
replies
1.3k
views
Tool:
Book: GNU Parallel 2018 - for beginners and advanced users
tool
ngs
parallel
Tool
2.5 years ago by
ole.tange
★ 4.0k
14
votes
17
replies
4.5k
views
8 follow
Parallel Computing With Key/Value Stores (Multiple Writes)
parallel
database
updated 2.6 years ago by
amirouche.boubekki
▴ 10 • written 10.0 years ago by
Sequencegeek
▴ 740
10
votes
2
replies
4.4k
views
Bwa: Number Of Threads
bwa
next-gen
sequencing
parallel
hardware
updated 2.6 years ago by
Ram
32k • written 10.9 years ago by
Pierre Lindenbaum
135k
4
votes
16
replies
3.6k
views
How to let WGCNA use multiple cores
WGCNA
multe-thread
parallel
updated 2.7 years ago by
yplee614
• 0 • written 4.0 years ago by
syrttgump
▴ 40
3
votes
13
replies
3.9k
views
Trim_galore on multiple fast.qz files: syntax problem
nsg
trim_galore
gnu
parallel
2.8 years ago by
m98
▴ 300
4
votes
2
replies
935
views
Are there any GNU parallel or similar Shell/Bash code examples on how to run Snap and BWA aligners on a batch of paired .fastq files?
gnu
parallel
shell
snap
bwa
updated 3.0 years ago by
ATpoint
47k • written 3.0 years ago by
england_bioinformatics_team
▴ 20
2
votes
3
replies
972
views
Are there any working GNU parallel or similar Shell code examples on how to run Pilon, Prokka, VT and Snpeff tools on a batch of input files?
gnu
shell
parallel
prokka
snpeff
updated 3.0 years ago by
Joe
19k • written 3.0 years ago by
england_bioinformatics_team
▴ 20
6
votes
9
replies
4.5k
views
Using parallel with Mem
mem
BWA
Parallel
updated 3.1 years ago by
Korsocius
▴ 180 • written 7.0 years ago by
always_learning
★ 1.1k
8
votes
2
replies
1.3k
views
Running assemblies in parallel
parallel
Assembly
fastq
updated 3.2 years ago by
Joe
19k • written 3.2 years ago by
marit.hetland
▴ 50
0
votes
1
reply
827
views
How to apply bedtools intersect function with GNU parallel for bacth BED file comparison?
bedtools
parallel
intersection
updated 3.2 years ago by
ATpoint
47k • written 3.2 years ago by
texaswhiskey1969
• 0
0
votes
2
replies
863
views
How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?
convert2bed
bedops
parallel
updated 3.2 years ago by
jean.elbers
★ 1.6k • written 3.2 years ago by
texaswhiskey1969
• 0
2
votes
3
replies
2.0k
views
Why can't I use a GRanges txDb with clusterMap function? (as input or output)
R
genomicFeatures
parallel
clusterMap
3.3 years ago by
jhanks1981
▴ 10
2
votes
2
replies
849
views
Paralellize samtools piped with awk
parallel
samtools
3.4 years ago by
Korsocius
▴ 180
0
votes
2
replies
1.2k
views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
3.4 years ago by
lakhujanivijay
5.4k
4
votes
3
replies
846
views
Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?
gnu
parallel
snpeff
bedtools
prokka
updated 3.4 years ago by
WouterDeCoster
45k • written 3.4 years ago by
bioinformatics_bel
▴ 20
5
votes
0
replies
1.4k
views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
meme
slurm
parallelization
parallel
Tutorial
3.6 years ago by
Alex Reynolds
32k
0
votes
2
replies
788
views
What platform similar to Galaxy can handle multiple batch processing of bacterial genomes, mutation profiling and GWAS?
galaxy
platform
parallel
mutation profiling
gwas
updated 3.7 years ago by
colindaven
★ 2.7k • written 3.7 years ago by
bioinform
▴ 20
13
votes
11
replies
1.6k
views
6 follow
Is it possible to run variant calling software in parallel, are there any Shell and Python/R code examples available?
parallel
vcf
variant calling
updated 3.7 years ago by
ivivek_ngs
★ 5.1k • written 3.7 years ago by
bioinform
▴ 20
2
votes
4
replies
2.9k
views
Why DESeq2 in parallel mode is slower than normal?!
RNA-Seq
DESeq
Differential Expression
parallel
updated 3.9 years ago by
Michael Love
★ 2.2k • written 3.9 years ago by
ilikebing2000
▴ 50
2
votes
3
replies
1.0k
views
how to run obisplit in parallel
obitools
obisplit
parallel
linux
fastq
3.9 years ago by
Roman Luštrik
▴ 120
5
votes
4
replies
2.5k
views
parse error with samtools
samtools
linux
parallel
4.1 years ago by
a.rex
▴ 250
105 results • Page
1 of 3
Recent Votes
Comment: why my volcano plot looks strange?
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Comment: What to put in my Github
Comment: What to put in my Github
Comment: What to put in my Github
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Comment: Trimmomatic-0.36 not finding adapter directory
by
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99k
Order of `fastq` file names is important for `trimmomatic`. Make sure that is correct.<br> Does `ls -lh /usr/local/bin/Trimmomatic-0.36/` …
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No love for [Tablet][1]? I'm quite surprised to not see it mentioned here. Of course, IGV is the classic, and Tablet is a bit simpler than …
Comment: How to download raw sequence data from GEO/SRA
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I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ?
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15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
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good luck!
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gtechbio
▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis
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gtechbio
▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
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▴ 120
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
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anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
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anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
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72k
^^ this
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7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Comment: why my volcano plot looks strange?
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15k
is it `log10p` or `-log10p` on y-axis?
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▴ 120
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
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