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352 results • Page
3 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
178
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
7 days ago by
Minh
• 0
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
7 days ago by
applepie
• 0
0
votes
6
replies
407
views
Download Panther entry list
PANTHER
7 days ago by
Nicolas
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 7 days ago by
Ram
43k • written 7 days ago by
Anisha
• 0
0
votes
0
replies
172
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
7 days ago by
sakura
• 0
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 7 days ago by
Ram
43k • written 7 days ago by
joseph.landry
▴ 50
0
votes
1
reply
199
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Smilesky
• 0
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
6 days ago by
tujuchuanli
▴ 100
2
votes
1
reply
208
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 7 days ago by
Ram
43k • written 8 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
136
views
Tool for power calculation in GWAS for quantative trait
trait
quantative
power
calculation
GWAS
8 days ago by
chevivien
▴ 90
1
vote
1
reply
279
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 7 days ago by
dthorbur
★ 1.7k • written 8 days ago by
ekirsch
• 0
1
vote
3
replies
252
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 8 days ago by
GenoMax
140k • written 8 days ago by
Sony
▴ 10
0
votes
1
reply
186
views
PEAR seems to have sense to me
PEAR
updated 8 days ago by
GenoMax
140k • written 8 days ago by
ManuelDB
▴ 80
0
votes
1
reply
171
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 8 days ago by
Pierre Lindenbaum
160k • written 8 days ago by
tien
▴ 10
0
votes
1
reply
159
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 7 days ago by
ATpoint
81k • written 8 days ago by
QX
• 0
0
votes
0
replies
149
views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
9 days ago by
bgbs
• 0
0
votes
0
replies
137
views
Motif analysis by HOMER
Homer
9 days ago by
daffodil
▴ 10
1
vote
2
replies
545
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
8 days ago by
e.r.zakiev
▴ 170
0
votes
0
replies
133
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
9 days ago by
Bioinfo
▴ 20
0
votes
1
reply
176
views
Resources regarding Proteomics (In-Silico)
proteomics
docking
protein
molecular-simulation
updated 9 days ago by
Ram
43k • written 9 days ago by
Saurabh
• 0
1
vote
0
replies
143
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
9 days ago by
Paula
▴ 10
0
votes
5
replies
407
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
1
vote
5
replies
410
views
Haddock 2.4
Protein
Docking
updated 8 days ago by
dthorbur
★ 1.7k • written 10 days ago by
Preeti
• 0
1
vote
0
replies
110
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
9 days ago by
marie.harmel
▴ 10
0
votes
1
reply
158
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 9 days ago by
Pierre Lindenbaum
160k • written 9 days ago by
Vullnet
• 0
0
votes
0
replies
115
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
10 days ago by
mhale
• 0
0
votes
0
replies
126
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 10 days ago by
Ram
43k • written 10 days ago by
shasabhi1
• 0
0
votes
0
replies
125
views
Genotype simulation
gwas
simulation
sim1000
updated 10 days ago by
Ram
43k • written 10 days ago by
Eliza
▴ 30
0
votes
0
replies
107
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
10 days ago by
kopelol
▴ 20
1
vote
1
reply
175
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 9 days ago by
Corentin
▴ 600 • written 10 days ago by
s.may-wilson
▴ 50
1
vote
3
replies
254
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 10 days ago by
dsull
★ 5.7k • written 10 days ago by
newuser2024
• 0
0
votes
2
replies
233
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
10 days ago by
Filip
• 0
0
votes
2
replies
196
views
FASTA/FASTQ files of fetal Aneuploids
nipt
10 days ago by
lolbye_1
• 0
0
votes
0
replies
127
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
11 days ago by
润达
• 0
0
votes
1
reply
172
views
BRIG coverage.graph issues
BRIG
sam
updated 11 days ago by
Pierre Lindenbaum
160k • written 11 days ago by
dlera.lozano
• 0
0
votes
0
replies
130
views
How to generate a comparative map using CGview?
genome
map
CGView
11 days ago by
marongiu.luigi
▴ 710
0
votes
0
replies
145
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
11 days ago by
amy__
▴ 160
1
vote
2
replies
442
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
10 days ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
238
views
Upset plot
upsetplot
10 days ago by
Chris
▴ 260
0
votes
1
reply
205
views
Are there any tools for mutational analysis of viruses?
virus
updated 10 days ago by
Ram
43k • written 12 days ago by
joey
▴ 10
0
votes
1
reply
254
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 12 days ago by
Arton
• 0 • written 14 days ago by
Samuel
▴ 20
0
votes
0
replies
141
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
12 days ago by
Arton
• 0
2
votes
2
replies
293
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
5 days ago by
bioinfo_enthusiast
• 0
1
vote
0
replies
148
views
How should I regenotype VCFs using vg?
vg
12 days ago by
Ricky
▴ 10
1
vote
2
replies
247
views
What GC content should I expect?
RNA-seq
GC-content
updated 12 days ago by
ATpoint
81k • written 12 days ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
136
views
stat test
stattest
chi2
updated 12 days ago by
GenoMax
140k • written 12 days ago by
NLL
• 0
0
votes
0
replies
163
views
Anvio HMM source campbell_et_al
anvio
updated 10 days ago by
Ram
43k • written 13 days ago by
Hayler Edu
▴ 40
0
votes
1
reply
226
views
Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig
UCSC
updated 13 days ago by
Pierre Lindenbaum
160k • written 13 days ago by
eeb74
• 0
0
votes
1
reply
222
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 13 days ago by
Pierre Lindenbaum
160k • written 13 days ago by
eeb74
• 0
1
vote
1
reply
247
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 13 days ago by
GenoMax
140k • written 13 days ago by
geocarvalho
▴ 360
352 results • Page
3 of 8
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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