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118,603 results • Page
3 of 2373
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
235
views
Pfam only identifies collagen
RNA-seq
lncRNA
updated 4 days ago by
Ram
44k • written 5 days ago by
Eduarda
• 0
0
votes
1
reply
146
views
How to split the aligned output from SortMeRNA into forward and reverse sequences
metatranscriptomic
sortmerna
updated 5 days ago by
Pierre Lindenbaum
163k • written 5 days ago by
eimanpharmacist
▴ 20
4
votes
5
replies
1.0k
views
6 follow
Remove part of a header in a fasta file
fasta
updated 5 days ago by
bk11
★ 2.9k • written 22 months ago by
kcl58759
• 0
0
votes
3
replies
253
views
rna-seq heatmap z-score calculation - TPM?
heatmap
rnaseq
updated 5 days ago by
ATpoint
84k • written 5 days ago by
lyc1ne
• 0
0
votes
1
reply
221
views
Sampling distribution of cosine similarity
RNA-seq
updated 5 days ago by
james.hawley
▴ 40 • written 6 days ago by
jayeshkumarsundaram
• 0
0
votes
1
reply
177
views
usually retained introns
intron
alternative
retention
splicing
updated 5 days ago by
Eric Lim
★ 2.1k • written 5 days ago by
adi.gershon1
• 0
5
votes
2
replies
249
views
How to Handle Unbalanced RNA-seq Data (710 vs. 15 Samples) Using DESeq2?
R
DESeq2
Unbalanced
RNA-seq
groups
updated 5 days ago by
Trivas
★ 1.8k • written 5 days ago by
Joe Kherery
▴ 140
3
votes
3
replies
378
views
Benchmark hg19 vcf by hs37d5 vcf
hs37d5
benchmark
hg19
GIAB
updated 5 days ago by
Pierre Lindenbaum
163k • written 10 days ago by
ThomasLam
• 0
0
votes
1
reply
292
views
How do you compare HLA allele frequencies between two populations?
allele-frequency
HLA
updated 5 days ago by
dthorbur
★ 2.4k • written 8 days ago by
Moschi
• 0
0
votes
4
replies
256
views
Heatmap for DEGs
seq
heatmap
RNA
5 days ago by
4732b159
• 0
1
vote
0
replies
130
views
News:
RNAseq and Single Cell Analysis Online Courses @ Edinburgh Genomics
RNA-seq
single-cell
workshop
updated 1 day ago by
Ram
44k • written 5 days ago by
Kat @ EdGe
▴ 10
0
votes
11
replies
549
views
Convert Gene ID To Gene Name
geneid
4 days ago by
min
• 0
3
votes
5
replies
358
views
Converting GFA to rGFA
gfa
2 days ago by
Ric
▴ 440
2
votes
5
replies
366
views
How to View Peaks from ChIP-seq Data generated using old reference genome (hg18)
R
Peak
ChIP-seq
updated 4 days ago by
ATpoint
84k • written 5 days ago by
DareDevil
★ 4.3k
0
votes
0
replies
133
views
Blog:
Metagenomics: Host DNA Removal or Not?
sequencing.
shotgun
metagenomics.
metagenomic
6 days ago by
Novogene
▴ 450
6
votes
8
replies
482
views
How to perform BLASTn on a large 348kb phage genome?
BLASTn
updated 5 days ago by
GenoMax
145k • written 6 days ago by
inamswati09
• 0
0
votes
2
replies
770
views
Apply Plink2 Score - Error Invalid chromosome code
plink
plink2
pgsc_calc
plink2score
updated 6 days ago by
Ruijiang HAN
▴ 10 • written 13 months ago by
h171linux
• 0
0
votes
4
replies
444
views
PLINK error doing a GWAS
phenotype
PLINK
covariates
association
GWAS
updated 6 days ago by
chrchang523
11k • written 8 days ago by
david.badenas.01
• 0
1
vote
6
replies
476
views
Analyzing PCA Clustering from PLINK Output
plink
5 days ago by
Smriti
▴ 30
3
votes
10
replies
630
views
Current best practive to liftOver many SNVs from hg19 to GRCh38
liftOver
updated 4 days ago by
Giulio Genovese
▴ 530 • written 6 days ago by
User 7754
▴ 260
4
votes
4
replies
408
views
gene naming
gene-names
ensembl
blast
updated 6 days ago by
Kevin Blighe
88k • written 16 days ago by
sasogalaxy90
▴ 10
1
vote
3
replies
407
views
Affymetrix microarray
gene-expression
probes
microarray
updated 6 days ago by
Ram
44k • written 16 days ago by
Shaimaa Gamal
▴ 10
0
votes
2
replies
326
views
Why does 1 variant produce 3 genes as a result?
GATK
SnpEff
updated 6 days ago by
Kevin Blighe
88k • written 26 days ago by
mgranada3
▴ 30
0
votes
4
replies
501
views
6 follow
Batch correction in RNAseq
RNA-seq
batch-correction
updated 6 days ago by
Kevin Blighe
88k • written 20 days ago by
Esraa
• 0
1
vote
1
reply
288
views
WGCNA - dendogram: How to interpret alterations of clusters
clustering
transcriptomics
WGCNA
rna
updated 6 days ago by
Ram
44k • written 10 days ago by
christiantd
• 0
0
votes
1
reply
304
views
Batch Effect Correction in RNA-seq Data Using SVA and DESeq2
SVA
Batch
DESeq2
RNA-seq
updated 6 days ago by
Kevin Blighe
88k • written 9 days ago by
Nelo
▴ 20
0
votes
0
replies
113
views
News:
Phylogenomics course
Multispecies-Coalescent-Model
Bayesian-Inference
Phylogenomics
Divergence-Time
Maximum-Likelihood
updated 6 days ago by
Ram
44k • written 6 days ago by
carlopecoraro2
★ 2.6k
1
vote
1
reply
179
views
Ethnicity information in GTEx dataset
metadata
gtex
updated 5 days ago by
GenoMax
145k • written 6 days ago by
husensofteng
▴ 410
1
vote
1
reply
186
views
How can I flag possible errors in the handbook collection?
Feedback
updated 6 days ago by
Pierre Lindenbaum
163k • written 6 days ago by
Fanta
▴ 10
0
votes
2
replies
276
views
RNA-seq and Chip Seq alignment
ChIP-seq
RNA-seq
alignment
updated 7 days ago by
Ram
44k • written 7 days ago by
alphaflylizard
• 0
12
votes
6
replies
7.5k
views
Download Hg18 Snp Database
snp
updated 7 days ago by
DareDevil
★ 4.3k • written 13.4 years ago by
Ardmore
▴ 140
4
votes
4
replies
478
views
Microbial PacBio metagenomes and MAG pipeline (assembly/binning) METABAT
binning
mag
pacbio
metabat
updated 8 days ago by
dportik
▴ 40 • written 8 days ago by
l.gallucci
▴ 20
0
votes
0
replies
341
views
Job:
Job opening for a Computational Biologist position at Weill Cornell Medical College, New York , USA
Computational-Genomics
Cornell
Transcriptomics
GI-Oncology
updated 7 days ago by
Ram
44k • written 8 days ago by
mas9313
• 0
1
vote
10
replies
606
views
ncRNA database for mus
contamination
ncRNA
sequencing
updated 6 days ago by
Jack Tierney
▴ 400 • written 8 days ago by
tommy
▴ 40
0
votes
1
reply
266
views
Seurat V5 Subscript Out of Bounds Error
Seurat
scRNA
updated 8 days ago by
bk11
★ 2.9k • written 8 days ago by
KokiBio
• 0
1
vote
0
replies
203
views
News:
Course - Machine Learning for Multi-Omics Integration
Machine-Learning
Big-Data
Multi-Omics
Data-Integration
Deep-Learning
updated 8 days ago by
Ram
44k • written 8 days ago by
carlopecoraro2
★ 2.6k
0
votes
4
replies
643
views
Subset Seurat Object based on metadata
Seurat
updated 8 days ago by
Ram
44k • written 12 weeks ago by
Bine
▴ 60
1
vote
4
replies
394
views
Overlapping reads between two BED windows
samtools
bam
bedtools
coverage
3 days ago by
pablo
▴ 310
0
votes
0
replies
181
views
Are there reliable assays other than genome sequencing, to measure tumor heterogeneity?
NGS
tumor-heterogeneity
WGS
updated 8 days ago by
Ram
44k • written 8 days ago by
anubratadas
▴ 20
1
vote
1
reply
215
views
Gene Regulatory Network Inference Data Needed
GRN
scATAC-SEQ
scRNA-SEQ
Single-Cell
Gene-Regulatory-Networks
updated 8 days ago by
Ram
44k • written 8 days ago by
Manuel Sokolov Ravasqueira
▴ 110
1
vote
1
reply
225
views
Remove microbes(cobionts) contamination: before or after insect de novo genome assembly?
contamination
genome
assembly
updated 8 days ago by
Philipp Bayer
8.7k • written 8 days ago by
hankool
• 0
2
votes
9
replies
4.2k
views
6 follow
Error Muscle alignment (msa package, through Rscript)
msa
r
muscle
updated 8 days ago by
ulrich.bodenhofer
• 0 • written 4.3 years ago by
alnam
▴ 10
1
vote
1
reply
215
views
Metatranscriptome pipeline: taxonomy and functional recover
metatranscriptome
pipeline
phyloflash
updated 5 days ago by
jeevii
• 0 • written 8 days ago by
l.gallucci
▴ 20
2
votes
5
replies
501
views
SNPs are not detected.
bcftools
SNP
WGS
updated 5 days ago by
Pierre Lindenbaum
163k • written 8 days ago by
R
▴ 10
2
votes
5
replies
360
views
Cutadapt&FastQC:sequence length disturbution failed after adapter trimming
disturbution
cutadapt
adapter
trimming
fastqc
updated 8 days ago by
dsull
★ 6.8k • written 8 days ago by
ashaneev07
▴ 20
0
votes
2
replies
254
views
ONT Improved RCA Barcoded Plasmid Sequencing
ONT
plasmid-sequencing
nanopore
ngs
updated 8 days ago by
Ram
44k • written 9 days ago by
thewiggler
• 0
0
votes
1
reply
302
views
DEseq2 interactions
Deseq2
updated 9 days ago by
Ram
44k • written 9 days ago by
drajangirija
▴ 10
2
votes
4
replies
401
views
Genotype File
Genotype
updated 9 days ago by
dsull
★ 6.8k • written 9 days ago by
goyal.shiwali
▴ 20
2
votes
4
replies
376
views
bcftools AA annotation failing
bcftools
vcf
ancestral-allele
8 days ago by
Whirlingdaf
▴ 60
1
vote
8
replies
535
views
Alignment of multiple files using STARSolo
STARSolo
9 days ago by
otieno43
▴ 30
118,603 results • Page
3 of 2373
Recent Votes
interpreting results from pathway analysis
A: What is the best way to rank genes for GSEA?
Answer: Generating consensus sequence from bam file
Answer: Generating consensus sequence from bam file
Comment: How to represent arbitrarily length kmer?
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
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Recent Awards •
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GenoMax
145k
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★ 6.8k
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6.8k
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Recent Replies
Comment: CuffDiff hangs at same point
by
chavanrenuka852
• 0
hi i have the same issue can you please provide me details how to create small ban file or how to provide subset of bams?
Comment: Script for Rstudio
by
Mensur Dlakic
★ 28k
I don't think anyone can help you until you tell us the error code.
Answer: blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) d
by
Mensur Dlakic
★ 28k
Don't know about GO and KEGG, but pretty sure there is no FASTA database for KOG. BLAST annotation is decidedly old-school, which I don't …
Comment: How to Convert Illumina Final Report File To Plink
by
Yan
• 0
Hi there, I have the same problem. did you success using SNPchimpRepo? Thanks!
Comment: GraphAligner/vg surject - alignment output nonsense?
by
stringsAsBaxters
• 0
Did you ever solve this? GraphAligner doesn't retain the base quality scores in the GAM output, see: https://github.com/maickrau/GraphA…
Comment: How to represent arbitrarily length kmer?
by
dwpeng
▴ 20
Hi, rob, thanks to your reply and I wrote a demo in Rust. Repo here: https://github.com/dwpeng/kmer
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
analyst
▴ 50
Okay thank you so much for making things clear. Raw counts were used for DGE analysis in DESeq2. Thanks a lot for saving time dsull!
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
dsull
★ 6.8k
OK, since you mention you're using DESeq2 for DGE analysis. DESeq2 uses counts (not FPKMs, not TPMs) for DGE. So if you're using DEseq2 co…
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
analyst
▴ 50
Thanks dsull, I am using deseq2 for DGE analysis
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
dsull
★ 6.8k
How are you performing the DGE analysis / what tool are you using for it?
Comment: Generating consensus sequence from bam file
by
skdv2522
• 0
Can anyone tell me why there is NNNNNN= no of gaps present in the final fasta file while converting bam into fasta with samtools consensus …
Comment: Generating consensus sequence from bam file
by
skdv2522
• 0
After conversion i got multiple NNNNN in the final fasta file. can anyone tell be why this happens
Comment: How to represent arbitrarily length kmer?
by
dwpeng
▴ 20
Thank you for the detailed answer. I will read KMC' and cuttlefish's source code.
Comment: GTF file
by
Juke34
8.6k
Have you looked at this issue in GitHub https://github.com/10XGenomics/cellranger/issues/133 If we can catch the sorting issue I could sol…
Answer: Doublets in scRNAseq analysis
by
OmnibusX
▴ 80
I often see a small population of B cells expressing CD3D in scRNAseq data, and I also do find some papers discussing this phenomenon. I s…
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