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116,006 results • Page
1 of 2321
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Votes
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0
votes
0
replies
5
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
6 minutes ago by
Lila M
★ 1.2k
0
votes
1
reply
15
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated just now by
Ram
43k • written 38 minutes ago by
Pumla
• 0
0
votes
1
reply
25
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 1 hour ago by
andrebolerbarros
• 0 • written 1 hour ago by
Christian
• 0
0
votes
1
reply
27
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated just now by
Ram
43k • written 1 hour ago by
Mohamed Abderrahmane
• 0
0
votes
0
replies
13
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
1 hour ago by
Broccoli
• 0
0
votes
0
replies
17
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
1 hour ago by
blur
▴ 280
0
votes
0
replies
32
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
2 hours ago by
liuyibin2005
• 0
49
votes
29
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 2 hours ago by
ATpoint
81k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
27
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial
SPOTlight
transcriptomic
logFC
deconvolution
2 hours ago by
M'zelle
• 0
0
votes
3
replies
95
views
calculate mismatch rate from VCF file
rate
VCF
mismatch
updated 10 minutes ago by
Pierre Lindenbaum
160k • written 8 hours ago by
Dora
▴ 10
0
votes
0
replies
31
views
Downloading a list of all refseq assembly ids, including supressed assembliey
refseq
ncbi
assembly
3 hours ago by
Bertalan_Takacs
▴ 90
2
votes
3
replies
247
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 3 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
113
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
updated 5 hours ago by
kayah
• 0 • written 6 hours ago by
Nitin
• 0
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
0
votes
0
replies
49
views
In scRNA, How should I set QC standards?
scRNA
QC
5 hours ago by
mnx0723
• 0
0
votes
0
replies
42
views
Annotation of Complex genomes using NCBI Genome Workbench
annotation
Genome
MAKER
Workbench
7 hours ago by
SAsciences
• 0
0
votes
2
replies
218
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
7 hours ago by
lingxue
• 0
0
votes
0
replies
54
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
8 hours ago by
Chris
▴ 260
1
vote
10
replies
682
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 8 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
256
views
FDR and Bonferroni
FDR
Bonferroni
updated 9 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
0
votes
1
reply
464
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 11 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
68
views
doing some ontology enrichment analysis
GO
12 hours ago by
aleksk779
• 0
2
votes
1
reply
158
views
Choosing an FC Threshold
statistics
rna-seq
updated 11 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
101
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 14 hours ago by
Mensur Dlakic
★ 26k • written 21 hours ago by
Ricard
• 0
0
votes
2
replies
135
views
novel and know mir156 and mir172
a
updated 11 hours ago by
gayachit
▴ 200 • written 14 hours ago by
Fadmo
• 0
0
votes
1
reply
87
views
Update R in Posit Workbench
R
Posit
updated 15 hours ago by
Ram
43k • written 16 hours ago by
Nitin
• 0
2
votes
8
replies
224
views
Piping samtools to R
R
NGS
bash
samtools
16 hours ago by
joe
▴ 470
8
votes
6
replies
372
views
Pangenome of plant
pangenome
plant
updated 17 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
167
views
vg call is time consuming
vg
17 hours ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 17 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
365
views
STAR aligner options
STAR
1 hour ago by
theophile
• 0
2
votes
3
replies
499
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 19 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
285
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 18 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
142
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
13 hours ago by
Ankit
▴ 500
0
votes
1
reply
93
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 18 hours ago by
Yogi
▴ 70 • written 19 hours ago by
Ronin
• 0
0
votes
0
replies
71
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 18 hours ago by
Ram
43k • written 19 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
73
views
Number of pathway result from GSVA
GSVA
20 hours ago by
Chris
▴ 260
0
votes
1
reply
108
views
How can I remove duplicate SNP?
plink
updated 20 hours ago by
iraun
6.2k • written 20 hours ago by
Zhennan
• 0
0
votes
1
reply
120
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 18 hours ago by
Ram
43k • written 20 hours ago by
Hajar
• 0
0
votes
0
replies
71
views
Creating a custom ontology for peptides
ontology
peptide
20 hours ago by
Mathew
• 0
0
votes
3
replies
184
views
convert cds to seurat object
R
monocle3
seurat
updated 10 minutes ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
72
views
GSEA number dimension of expression dataset
GSEA
21 hours ago by
edoardofilippi1998
• 0
0
votes
2
replies
207
views
Limma compare between 3 conditions vs 2 conditions
Limma
20 hours ago by
Chris
▴ 260
0
votes
0
replies
79
views
single cell data integration approach
comparison
integration
pairwise
singlecell
22 hours ago by
Jay
• 0
0
votes
3
replies
205
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
20 hours ago by
sarahmanderni
▴ 100
1
vote
1
reply
197
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 23 hours ago by
GenoMax
140k • written 1 day ago by
JH
• 0
0
votes
2
replies
145
views
Error with goodSamplesGenes()
R
WGCNA
18 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
88
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
300
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 12 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
139
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
116,006 results • Page
1 of 2321
Recent Votes
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
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104k
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blur
▴ 280
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ATpoint
81k
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Recent Replies
Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
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