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115,827 results • Page
1 of 2317
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0
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193
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Ribo and RNA seq analysis
RNA-seq
genomics
Ribo-seq
just now by
Manu Ayllon
• 0
0
votes
0
replies
5
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
10 minutes ago by
sarahmanderni
▴ 100
0
votes
0
replies
4
views
Resources regarding Proteomics (In-Silico)
proteomics
protein
molecular
simulation
docking
10 minutes ago by
Saurabh
• 0
0
votes
0
replies
6
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
10 minutes ago by
Марта
• 0
0
votes
0
replies
16
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
31 minutes ago by
Paula
• 0
0
votes
2
replies
143
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
1 hour ago by
Learner
• 0
0
votes
1
reply
53
views
why there is an asterisk symbol at the end of each proteins sequences offasta files in the Breaker3 output FASTA file?
gtf
breaker3
protein-seq
updated 28 minutes ago by
GenoMax
140k • written 1 hour ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
17
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
2 hours ago by
samyu.senthil
• 0
0
votes
2
replies
149
views
Haddock 2.4
Protein
Docking
2 hours ago by
Preeti
• 0
0
votes
0
replies
27
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
2 hours ago by
b.contreras.moreira
▴ 10
0
votes
2
replies
135
views
Beagle Phasing and Imputation
imputation
phasing
beagle
2 hours ago by
Duarte Molha
▴ 240
1
vote
0
replies
27
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
3 hours ago by
marie.harmel
▴ 10
0
votes
2
replies
123
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 3 hours ago by
fracarb8
★ 1.5k • written 13 hours ago by
bgbs
• 0
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 3 hours ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
0
votes
1
reply
54
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 3 hours ago by
Pierre Lindenbaum
160k • written 3 hours ago by
Vullnet
• 0
0
votes
2
replies
90
views
DEG (Differential expression gene) analysis
DEG
R
updated 4 hours ago by
dsull
★ 5.6k • written 4 hours ago by
sooni
▴ 20
0
votes
1
reply
107
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 4 hours ago by
Zhenyu Zhang
★ 1.1k • written 15 hours ago by
kcarey
• 0
791
votes
167
replies
138k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.5k • written 7.3 years ago by
Istvan Albert
100k
0
votes
0
replies
40
views
News:
Online course: Adaptation Genomics
StructuralVariants
Selection
AdaptationGenomics
PopulationStructure
5 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
37
views
News:
Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics
Pangenomics
5 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
68
views
library(scater)
sce
scRNASeq
scater
updated 6 hours ago by
Mensur Dlakic
★ 26k • written 7 hours ago by
Nitin
• 0
0
votes
1
reply
165
views
Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
updated 9 hours ago by
swbarnes2
14k • written 12 hours ago by
Shelby
• 0
0
votes
4
replies
226
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 9 hours ago by
Doomhammer
• 0 • written 23 hours ago by
ben@f
▴ 10
0
votes
1
reply
496
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 10 hours ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
4
votes
4
replies
207
views
Differential express genes in imbalance groups
Limma
11 hours ago by
Chris
▴ 260
2
votes
1
reply
106
views
basal gene expression level
RNA-Seq
updated 15 hours ago by
LChart
3.8k • written 15 hours ago by
Francois Piumi
▴ 40
0
votes
0
replies
65
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
15 hours ago by
mhale
• 0
1
vote
1
reply
128
views
Seurat 5 integration
integration
seurat
updated 16 hours ago by
jared.andrews07
★ 16k • written 18 hours ago by
sarahmanderni
▴ 100
3
votes
5
replies
211
views
scRNAseq normalization
scRNA-seq
SCT
updated 1 hour ago by
ATpoint
81k • written 17 hours ago by
sarahmanderni
▴ 100
3
votes
7
replies
1.2k
views
7 follow
Transcription Start Site
TSS
updated 8 hours ago by
Ming Tommy Tang
★ 3.8k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
0
votes
0
replies
70
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 17 hours ago by
Ram
43k • written 17 hours ago by
shasabhi1
• 0
0
votes
0
replies
73
views
Genotype simulation
gwas
simulation
sim1000
updated 19 hours ago by
Ram
43k • written 19 hours ago by
Eliza
▴ 30
0
votes
0
replies
68
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 19 hours ago by
Ram
43k • written 19 hours ago by
matt.a.bennett25890
• 0
4
votes
2
replies
137
views
Problem with .bed file
cygwin64
bed
PLINK
updated 16 hours ago by
Ram
43k • written 19 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
177
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO
clusterProfiler
updated 20 hours ago by
Dunois
★ 2.5k • written 1 day ago by
TIANTHING JESTLIN
• 0
0
votes
0
replies
76
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
20 hours ago by
kopelol
▴ 20
4
votes
2
replies
239
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
5 hours ago by
경준
▴ 20
1
vote
2
replies
242
views
Trim Galore: Automatic detection of adapters
trimgalore
15 hours ago by
Daniel
▴ 30
1
vote
1
reply
110
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 2 hours ago by
Corentin
▴ 600 • written 22 hours ago by
s.may-wilson
▴ 50
1
vote
3
replies
200
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 8 hours ago by
dsull
★ 5.6k • written 22 hours ago by
newuser2024
• 0
0
votes
4
replies
232
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 19 hours ago by
SequenceServer
▴ 140 • written 1 day ago by
Luca
• 0
0
votes
2
replies
156
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
19 hours ago by
Filip
• 0
1
vote
1
reply
111
views
turning old shell ncbi querys into url querys
eutils
ncbi
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Guelakais
• 0
0
votes
1
reply
455
views
ArchR Doublet Inference to Signac
Signac
scATAC-seq
ArchR
updated 1 day ago by
fracarb8
★ 1.5k • written 13 months ago by
bioinformatics.girl
▴ 20
0
votes
2
replies
158
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
23 hours ago by
Niharika
• 0
3
votes
10
replies
629
views
t-test in two groups, multiple rows
R
t-test
11 hours ago by
sooni
▴ 20
3
votes
4
replies
1.3k
views
sam.gz files to bam using samtools
RNA-Seq
samtools
updated 1 day ago by
robertoalbanese.bioinfo
• 0 • written 12 months ago by
tikshyadav19
• 0
0
votes
4
replies
211
views
error in wigToBigWig while converting mappability to bedgraph
mappability
gem
bedgraph
wigToBigWig
3 hours ago by
Dora
▴ 10
0
votes
0
replies
105
views
Forum:
Field of Study in Computational Biology
Genomics
Computational-Biology
PhD
updated 19 hours ago by
Ram
43k • written 1 day ago by
Mohammed
• 0
0
votes
2
replies
168
views
FASTA/FASTQ files of fetal Aneuploids
nipt
1 day ago by
lolbye_1
• 0
115,827 results • Page
1 of 2317
Recent Votes
Comment: BAM to CRAM and BAM recover with smaller size
Comment: Average expression of a sample in single-cell data
A: Normalize FPKM values for cross-sample comparisons?
Answer: ColabFold
C: How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?
Troubleshooting a REGENIE sex-stratified GWAS
ENVO Ontology to Annotate Plain Text
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Popular Question
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padwalmk
▴ 140
Popular Question
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dodausp
▴ 180
Scholar
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Devon Ryan
104k
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inedraylig
▴ 60
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Ming Tommy Tang
★ 3.8k
Popular Question
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aUser
▴ 30
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Gordon Smyth
★ 6.9k
Recent Replies
Answer: Ribo and RNA seq analysis
by
Manu Ayllon
• 0
I got it making use of blastn, creating first a database with the RNA sequences and doing blast with the Ribo-seq sequences as query. The p…
Comment: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Comment: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
Corentin
▴ 600
Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Comment: Beagle Phasing and Imputation
by
Duarte Molha
▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
Answer: error in wigToBigWig while converting mappability to bedgraph
by
Pierre Lindenbaum
160k
remove the spaces from your "chrom" key variableStep chrom=NT_173277 span=5 or may be quote the chrom variableStep chrom="NT_173277.1 C…
Comment: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
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