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122,013 results • Page
298 of 2441
Sort: Rank
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Votes
Replies
3
votes
3
replies
1.2k
views
Same pipeline produces different results
Cellranger
scRNaseq
genome
countmatrix
updated 2.6 years ago by
Jesse
▴ 880 • written 2.7 years ago by
Tadeoye
▴ 30
1
vote
2
replies
961
views
Do I need to merge files after downloading them from SRA?
rna-seq
sra
2.7 years ago by
bioinfo
▴ 160
0
votes
1
reply
1.2k
views
Signac/DeepTools data exchange
SIgnac
Seurat
r
DeepTools
updated 2.5 years ago by
DARLOR
▴ 10 • written 2.7 years ago by
ARP
▴ 10
0
votes
1
reply
741
views
GATK HaplotypeCaller combine info from two BAM into one line in vcf (not divide into samples column)
HaplotypeCaller
GATK
VCF
updated 2.7 years ago by
Pierre Lindenbaum
166k • written 2.7 years ago by
kamanovae
▴ 100
0
votes
5
replies
1.4k
views
Free access European cohort study
GWAS
PRS
updated 2.7 years ago by
Sam
★ 4.8k • written 2.7 years ago by
nyanovsky
• 0
3
votes
4
replies
2.1k
views
RSEM calculate-expression has only one sample in .isoforms.results file
RSEM
RNA-seq
STAR
2.7 years ago by
Daniel
▴ 40
1
vote
4
replies
2.3k
views
Repeat masking for genome annotation
masking
annotation
repeat
2.6 years ago by
liorglic
★ 1.5k
2
votes
1
reply
914
views
How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`?
deepTools
updated 2.7 years ago by
Trivas
★ 1.9k • written 2.7 years ago by
Dan
▴ 180
1
vote
0
replies
1.3k
views
Job:
Computational Research Scientist I or II, Metabolic Network Modeling (Hybrid)
Toxicogenomics
Metabolicnetworks
Metabolomics
2.7 years ago by
Diwan
▴ 650
5
votes
5
replies
1.2k
views
Convert genomic files from known Gigabases(# of bases) to gigabytes
gigabases
gigabytes
genomics
updated 2.7 years ago by
GenoMax
154k • written 2.7 years ago by
datanerd
▴ 520
22
votes
8
replies
48k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 2.1 years ago by
Bioinformatics_NewComer
▴ 330 • written 13.2 years ago by
bioinfo
▴ 840
2
votes
1
reply
568
views
Improve coverage in callvariants.sh
bbtools
callvariants
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Hayler Edu
▴ 40
0
votes
0
replies
392
views
Chromatin state identification
Chromatin
SNP
2.7 years ago by
Sara
• 0
0
votes
0
replies
438
views
Nearest neighbors from a determinate gene in the module
WGCNA
igraph
2.7 years ago by
cardon.chc
• 0
0
votes
0
replies
518
views
Q: --methimpute not recognized by Bismark and run in single core
next-gen
bismark
RNA-seq
updated 2.6 years ago by
Ram
45k • written 2.7 years ago by
sam
• 0
1
vote
0
replies
1.2k
views
Herald:
The Biostar Herald for Wednesday, February 15, 2023
herald
2.7 years ago by
Biostar
3.6k
0
votes
0
replies
525
views
metagenomics project - identification of species
metagenomics
wimp
taxonomy
epi2me
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
aziznasr1920
▴ 10
3
votes
3
replies
4.5k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC
TCGABiolinks
STAR
updated 2.7 years ago by
Ram
45k • written 3.5 years ago by
DareDevil
★ 4.4k
0
votes
1
reply
851
views
differential expression analysis
RT-PCR
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Vikram
• 0
10
votes
19
replies
4.3k
views
Redirecting pHMMER output to /dev/null
annotation
protein
HMMER
gene
genome
updated 2.7 years ago by
Md
▴ 10 • written 6.5 years ago by
Morgan S.
▴ 90
0
votes
1
reply
1.2k
views
UKBiobank / DNANexus. Working with WDL and directories.
wdl
workflow
dnanexus
ukbiobank
2.7 years ago by
Pierre Lindenbaum
166k
9
votes
8
replies
4.8k
views
7 follow
What are Differentially Expressed Genes ?!!
FDR
DEG
p-value
logFC
updated 2.6 years ago by
Kevin Blighe
89k • written 2.7 years ago by
Sowmya Pulapet
▴ 70
0
votes
1
reply
725
views
PLINK ped file
ped
GWAS
summarystats
PLINK
map
updated 2.7 years ago by
Fabio Marroni
★ 3.0k • written 2.7 years ago by
loy_loy
▴ 10
1
vote
3
replies
1.1k
views
Linux server Vs Linux pc
Linux
server
analysis
Transcriptomic
updated 2.7 years ago by
Joe
22k • written 2.7 years ago by
Vikram
• 0
0
votes
1
reply
741
views
How to identify which are the the pre therapy samples?
data
RNA-seq
updated 2.7 years ago by
Basti
★ 2.1k • written 2.7 years ago by
AlexStar
▴ 200
0
votes
1
reply
787
views
ValueError: not enough values to unpack (expected 2, got 1)
clinker
updated 2.7 years ago by
lacb
▴ 120 • written 2.7 years ago by
Neel
▴ 20
1
vote
1
reply
1.2k
views
ggVennDiagram help
r
ggVennDiagram
updated 2.7 years ago by
Basti
★ 2.1k • written 2.7 years ago by
Dr.
• 0
0
votes
1
reply
723
views
Gene coverage issue in HG38
GRCh38
BWA-mem
2.7 years ago by
rajesh.msch
• 0
1
vote
2
replies
1.1k
views
CABSDock issue:DSSP not found
CABSDock
DSSP
ubuntu
2.7 years ago by
Farha
• 0
6
votes
6
replies
5.0k
views
What specifications of laptop should I buy for bioinformatics?
Microbiome
updated 2.7 years ago by
Mensur Dlakic
★ 30k • written 2.7 years ago by
yonghyun09
• 0
0
votes
4
replies
1.3k
views
R error when trying to run ssGSEA
ssGSEA
R
2.7 years ago by
3129821299
• 0
3
votes
1
reply
782
views
Extract Interactions using paxtoolsr from Pathway Commons
r
pathway
updated 2.7 years ago by
cannin
▴ 350 • written 2.7 years ago by
Norma
▴ 10
2
votes
2
replies
1.3k
views
All vs all blast - unexpected results
alignment
seg
blastp
2.7 years ago by
timothy.kirkwood
▴ 140
2
votes
2
replies
1.2k
views
Annotation of 16S rDNA identified bacteria
rDNA
16s
updated 2.7 years ago by
Mensur Dlakic
★ 30k • written 2.7 years ago by
Mahnoor
• 0
1
vote
4
replies
1.3k
views
Error while converting ExpressionSet format to SingleCellExperiment format?
SingleCellExperiment
ExpressionSet
R
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
shuaizh117
▴ 10
1
vote
1
reply
1.8k
views
prokka --setupdb issue
gene-annotation
prokka
updated 2.6 years ago by
Ram
45k • written 2.7 years ago by
littlemicrobiologist
• 0
2
votes
2
replies
1.3k
views
vcf to bcf conversion
vcf
bcftools
bcf
updated 2.3 years ago by
Ram
45k • written 2.7 years ago by
solarchan7
• 0
0
votes
0
replies
529
views
Using MGnify API
API
Metagenomic
updated 2.7 years ago by
GenoMax
154k • written 2.7 years ago by
aaggencc
• 0
3
votes
4
replies
1.4k
views
How much reads per cell for fusion detection with Nanopore ?
single-cell
fusion
nanopore
2.6 years ago by
Evan
▴ 250
0
votes
1
reply
706
views
Need help in applying LRT to my count abundance data
LRT
R
DESeq2
2.7 years ago by
rishav513
▴ 30
1
vote
1
reply
682
views
Variables in for loop
Trimmomatic
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Hayler Edu
▴ 40
0
votes
1
reply
743
views
Can ARIBA AMR tool be tweaked to support long reads inputs (eg-Oxford Nanopore)?
AMR
Oxford
Nanopore
ARIBA
updated 8 months ago by
AHerik
▴ 40 • written 2.7 years ago by
varunsreeraj
• 0
0
votes
1
reply
880
views
What is correct percentage of sense-stranded transcripts in directional de novo assemblies ?
Trinity
strand-specificity
RNA-seq
Transdecoder
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Lada
▴ 40
0
votes
1
reply
622
views
News:
Courses in March. -still a few seats available
Bioconductor
Genomics
R
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Physalia-courses
★ 2.7k
2
votes
1
reply
706
views
Distribution of DEGs according to gene length
distribution
RNA-seq
updated 2.7 years ago by
Ram
45k • written 2.7 years ago by
Marco Pannone
▴ 810
4
votes
2
replies
3.4k
views
How does enrichGO function calculated p-value?
clusterProfiler
p-value
ORA
DGE
R
updated 2.7 years ago by
Papyrus
★ 3.1k • written 2.7 years ago by
Ezequiel
▴ 10
15
votes
8
replies
8.8k
views
Encountering error when loading scanpy?
scanpy
single-cell
scRNA-seq
2.6 years ago by
bioinfo
▴ 160
1
vote
9
replies
2.9k
views
Obtaining bcf and vcf files and use bcf tool annotate
bcftools
updated 2.6 years ago by
Ram
45k • written 2.7 years ago by
anasjamshed
▴ 140
5
votes
1
reply
985
views
How to identify whether the sample is from only one person and whether the sample is tumor or normal
somatic
NGS
updated 2.7 years ago by
ATpoint
89k • written 2.7 years ago by
tan
▴ 10
0
votes
0
replies
722
views
updating annotation of illumina human methylation 450k data
minfi
methylation
450k
annotation
infinium
2.7 years ago by
eebloom
▴ 110
122,013 results • Page
298 of 2441
Recent Votes
A: Bam And Indexed Bam Files
Answer: How to create a phylogenetic tree from 30 VCF files
Comment: Reading AD and other genotype information from the VCF file
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
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★ 1.7k
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Answer: 1 vs 1 DEG analysis in scrna seq data
by
ATpoint
89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis
by
firestar
★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome.
by
michael.ante
★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
lieven.sterck
16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Ram
45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
ATpoint
89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info
by
ATpoint
89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue?
by
ATpoint
89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks
by
rfran010
★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample
by
cmdcolin
★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
aj123
▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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