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121,832 results • Page
604 of 2437
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
1.3k
views
EdgeR - Input for Analysis Functions (estimateDisp, exactTest, glmQLFit)
edgeR
R
4.1 years ago by
Noah E.
▴ 20
1
vote
1
reply
1.1k
views
How to change CpG methylation cutoffs in edgeR
R
updated 4.1 years ago by
iraia.munoa
▴ 130 • written 5.4 years ago by
embueno
• 0
1
vote
5
replies
2.6k
views
MUSCLE alignment - aligning whole genome with gene sequences
alignment
mega
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
manaswwm
▴ 570
5
votes
4
replies
3.1k
views
Error when using UpSetR package
UpSetR
R
4.1 years ago by
peter.berry5
▴ 60
18
votes
15
replies
21k
views
9 follow
Tools Parsing Ncbi Blast -M 7 Xml Output Format?
blast
xml
parsing
updated 4.1 years ago by
Yoann Pageaud
• 0 • written 14.4 years ago by
Lhl
▴ 760
0
votes
8
replies
1.9k
views
print only columns with data from every line
unix
awk
4.1 years ago by
HL
▴ 10
2
votes
12
replies
3.5k
views
Bowtie2 aligner
Bowtie2
alignment
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
priya.bmg
▴ 70
1
vote
2
replies
1.0k
views
Determine relative copy numbers of plasmids
mapping
bowtie2
samtools
coverage
4.1 years ago by
rororo
▴ 10
0
votes
1
reply
971
views
SNP density plot of aedes genome using bed file
density
Variant
ideograms
4.1 years ago by
anithanagaraj93
▴ 10
1
vote
0
replies
750
views
What is the importance of removing reads mapped to repetitive elements for downstream enrichment in RNAseq/CLIPseq?
Repetitive_elements
alignment
CLIPseq
RNAseq
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
Patrick
▴ 10
1
vote
1
reply
1.2k
views
How to get uniform data yields per barcode in nanopore sequencing
ONT
nanopore
updated 4.1 years ago by
samuel.a.odonnell
▴ 600 • written 4.1 years ago by
Irsan
★ 7.8k
0
votes
0
replies
1.1k
views
Job:
PhD student, PostDoc and Software Developer Positions at the interface of Mathematics and Life Science
postdoc
phd
Computational-Biology
Mathematics
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
emad-24
• 0
0
votes
0
replies
729
views
somatic variant calling with Mutect2
calling
somatic
Mutect2
variant
4.1 years ago by
Elisa
• 0
0
votes
0
replies
662
views
Forum:
Poll about a structured description of a tool, a pipeline
survey
pipeline
updated 2.2 years ago by
Ram
45k • written 4.1 years ago by
Anastasiya M
• 0
1
vote
11
replies
3.0k
views
How to merge folders that have similar (not the same) names, in a folder keeping as its name the common part of the name of the two folders
folders
merge
name-based
updated 4.1 years ago by
cpad0112
21k • written 4.1 years ago by
Mania
• 0
4
votes
5
replies
1.4k
views
6 follow
Gene prediction methods
Gene
prediction
updated 4.1 years ago by
GenoMax
153k • written 4.2 years ago by
Pratheep
▴ 150
1
vote
4
replies
2.3k
views
cellranger count aggregated to transcripts
cellranger
gtf
10x
updated 4.1 years ago by
benformatics
4.2k • written 4.1 years ago by
jomo018
▴ 730
1
vote
4
replies
2.0k
views
Paired-end to Single-end
bam
updated 4.1 years ago by
Kevin Blighe
89k • written 4.1 years ago by
kstangline
▴ 100
1
vote
4
replies
2.3k
views
extracting fasta sequence from fasta file with multiple genomes
bedtools
fasta
grep
updated 4.1 years ago by
cpad0112
21k • written 4.1 years ago by
ss3943
• 0
0
votes
0
replies
712
views
Repeat masking custom library not reading
masking
repeat
ngs
repeatmasker
4.1 years ago by
Shri hari
▴ 40
8
votes
10
replies
2.9k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid
protein
peptide
Reading
optimal
frames
4.1 years ago by
Luis999
▴ 20
0
votes
4
replies
2.2k
views
kissplice2reftranscriptome interpreting output
RNA-Seq
kissplice2reftranscriptome
kissplice
updated 4.1 years ago by
944908620
• 0 • written 7.6 years ago by
rares_lucaciu
• 0
0
votes
0
replies
949
views
PSMC parameter choosing (-t, -p)
psmc
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
clinnaeus
▴ 30
9
votes
5
replies
29k
views
7 follow
DESeq2 analysis for multiple conditions
RNA-Seq
DESeq2
updated 2.7 years ago by
Ram
45k • written 10.3 years ago by
eager_learner
▴ 60
0
votes
1
reply
1.5k
views
Help with installing Bayescan (Big Sur)
Installation
commandline
Bayescan
updated 4.1 years ago by
ATpoint
89k • written 4.1 years ago by
8bde229f
• 0
2
votes
2
replies
1.2k
views
Functional annotation by blast
trembl
Blast
nr
Functional_annotation
Blast2GO
4.1 years ago by
GenesisBio
• 0
0
votes
0
replies
1.6k
views
Job:
Senior Postdoctoral Research Fellow at Big Data Institute, University of Oxford
big
postdoc
genomics
data
4.1 years ago by
Shicheng Guo
★ 9.6k
0
votes
1
reply
1.5k
views
What does betaPrior do in DESEQ?
DESeq
RNAseq
updated 4.1 years ago by
i.sudbery
22k • written 4.1 years ago by
kirby199
• 0
0
votes
0
replies
923
views
Herald:
The Biostar Herald for Monday, July 26, 2021
herald
4.1 years ago by
Biostar
3.6k
0
votes
1
reply
919
views
Handling cultivars in transcriptome de novo assembly
transcriptomic
trinity
DGE
updated 4.1 years ago by
h.mon
35k • written 4.1 years ago by
DaneLukin
• 0
0
votes
1
reply
792
views
Quantify the effects of a gene list between datasets
scRNA-Seq
Comparison
RNA-Seq
4.1 years ago by
bioinf.questions
• 0
4
votes
4
replies
2.0k
views
RNA-seq for samples with RIN<3
RIN
Low
updated 7 months ago by
Emilie
▴ 10 • written 4.1 years ago by
mariam28071993
• 0
1
vote
1
reply
749
views
How can I extract duplicated rows for the same value and write them down in one row
bash
updated 4.1 years ago by
Ram
45k • written 4.1 years ago by
amal.elzemrany
▴ 30
3
votes
3
replies
2.0k
views
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist
metagenomics
prokaryotic
eukaryotic
gtdbtk
updated 4.1 years ago by
Mensur Dlakic
★ 29k • written 4.1 years ago by
O.rka
▴ 750
2
votes
2
replies
1.1k
views
Helper packages for differential gene expression analysis in R
dge
deseq2
RNA-seq
r
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
Dunois
★ 2.9k
0
votes
0
replies
618
views
How can I conduct GO/Pathway analysis in EdgeR when there is >1 value for each gene?
edgeR
R
4.1 years ago by
Noah E.
▴ 20
1
vote
0
replies
660
views
GO Term analysis
GO
updated 4.1 years ago by
Ram
45k • written 4.1 years ago by
snehu.sambare
▴ 10
1
vote
2
replies
1.8k
views
Merge regions in bedgraph file
bedgraph
4.1 years ago by
eoneill627
▴ 20
0
votes
0
replies
899
views
Paired Analysis in EdgeR
EdgeR
PairedAnalysis
4.1 years ago by
bryan.yankee27
• 0
1
vote
2
replies
964
views
Low similarity gene alignment
analysis
align
gene
updated 4.1 years ago by
Dunois
★ 2.9k • written 4.1 years ago by
Hsiangnan Cheng
• 0
0
votes
1
reply
998
views
metascape
list
gene
input
metascape
updated 4.1 years ago by
Ram
45k • written 4.1 years ago by
fionajcunningham
• 0
5
votes
5
replies
4.2k
views
Visualiation of samtools depth output in a plot
plot
depth
samtools
updated 3.9 years ago by
Carlo Yague
9.0k • written 4.1 years ago by
dominik.lagler
▴ 30
1
vote
3
replies
1.1k
views
ALT-aware autodetection of hg38.p13 in DRAGEN
alt
patch
alt-aware
dragen
hg38
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
Tal
• 0
0
votes
0
replies
1.1k
views
Error with CONVERTF mergeit program
plink
convertf
eigenstrat
4.1 years ago by
harmadikemil
• 0
2
votes
2
replies
1.1k
views
Filter vcf file based on the GTs of a single sample
bcftools
vcf
samtools
bcf
updated 4.1 years ago by
sbstevenlee
▴ 480 • written 4.1 years ago by
miguellarrazlopezdenovales
▴ 20
4
votes
6
replies
2.6k
views
6 follow
What is the best annotation tool?
VCF
annotation
updated 4.1 years ago by
colindaven
7.8k • written 4.1 years ago by
Sonia
• 0
0
votes
0
replies
978
views
Job:
Postdoctoral Fellowship in Bioinformatics and Liver Cancer Genomics
Cancer
NGS
Single-cell
genomics
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
waihungh
▴ 20
0
votes
0
replies
1.6k
views
Job:
PhD Scholarship in Bioinformatics and Liver Cancer Genomics
Cancer
NGS
Single-cell
genomics
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
waihungh
▴ 20
0
votes
0
replies
869
views
Job:
research assistant in bioinformatics at Essen University Hospital
metadata
Germany
Essen
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
christina.klaere
• 0
1
vote
6
replies
7.4k
views
How to write a .pdb file using Python
python
PDB
output
updated 4.1 years ago by
Nitin Narwade
★ 1.7k • written 4.1 years ago by
Jingtong
• 0
121,832 results • Page
604 of 2437
Recent Votes
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Split chromosome into smaller fragments to save memory when build xg and gcsa in
C: DiffBind error when calling dba.count
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
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Recent Replies
Answer: CDS prediction for newly assembled transcripts
by
Ales
• 0
We have recently developed a dedicated method [ORFanage][1] to address this specific issue in studies which already have detailed protein r…
Answer: Gene feature information missing in Stringtie merged assembly
by
Ales
• 0
We have also recently published a dedicated by-reference ORF assignment algorithm ([ORFanage][1]) which is designed largely to perform CDS …
Answer: Criteria for choosing variants
by
benformatics
4.2k
The whole question seems very confusing as if there is a substantial knowledge gap. Calling variants in tumor-normal pairs is relatively…
Comment: How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
by
GenoMax
153k
> Cannot run FragGeneScan. Please indicate the file directory in 'setting' file. Looks like you will need to add the. directory containing…
Comment: How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
by
Pallishree
• 0
i have run this command (maxbin2_env) [m5@mks1 FASTQ]$ /data/sms/home/m5/.conda/envs/maxbin2_env/bin/run_MaxBin.pl \ ? -contig /…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Arup Ghosh
3.4k
The `--nv` flag for apptainer is there?
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Arup Ghosh
3.4k
The GPUs have 24 GB memory each but only worked with the flag.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Pierre Lindenbaum
166k
it doesn't work with `--htvc-low-memory` (same error with 4.5.0-1 )
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
GenoMax
153k
`Parabrix` is not supported on multi-instance GPU's (MIG) so having that setting disabled is perfect.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
GenoMax
153k
That option is indicated for using a 16GB GPU. Was that the case or even though you had a >16 GB GPU, this option was needed to fix the err…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Arup Ghosh
3.4k
I faced a similar issue with Parabricks and version 4.3.0; using `--htvc-low-memory` resolved the problem.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Mensur Dlakic
★ 29k
Maybe this will help: https://stackoverflow.com/questions/67091056/gpu-allocation-in-slurm-gres-vs-gpus-per-task-and-mpirun-vs-srun
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in
by
Jordan M Eizenga
▴ 750
GCSA2 indexing is fairly demanding on disk space, so that can happen. I would generally recommend having 1-2 TB of disk availability if you…
Comment: how to start
by
shelkmike
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If you plan to become a professional bioinformatician, I don't recommend the approach suggested by Joe and Yura Grabovska (learning bioinfo…
Comment: vg input and output files
by
GenoMax
153k
Have you looked at this page: https://github.com/vgteam/vg/wiki/Basic-Operations There is a pipeline illustration on this page that shows …
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