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1,000 results • Page
2 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
874
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
5 days ago by
Mark
• 0
0
votes
0
replies
151
views
not best k value found
de
assemblly
assembly
novo
kmergenie
5 days ago by
shaileshdesai76
• 0
0
votes
0
replies
159
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
6 days ago by
Carmen
• 0
0
votes
0
replies
166
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
6 days ago by
pl23
• 0
0
votes
2
replies
272
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
1 day ago by
je71xusa
• 0
0
votes
2
replies
265
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 6 days ago by
Raony Guimarães
★ 1.3k • written 6 days ago by
ThePlaintiff
▴ 80
2
votes
8
replies
588
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
updated 2 days ago by
GenoMax
136k • written 8 days ago by
ian.will
▴ 10
5
votes
2
replies
239
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
5 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
192
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 6 days ago by
WouterDeCoster
47k • written 6 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
136
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
6 days ago by
WUSCHEL
▴ 720
0
votes
3
replies
282
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 1 day ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
0
replies
108
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
6 days ago by
Ngrin
• 0
0
votes
0
replies
120
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
7 days ago by
turcoa1
• 0
0
votes
0
replies
124
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
7 days ago by
alphaflylizard
• 0
0
votes
2
replies
255
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
6 days ago by
chscho
• 0
0
votes
0
replies
114
views
Trouble making a ggmsa alignment plot
R
ggmsa
7 days ago by
andre.arrudalima
▴ 30
0
votes
0
replies
107
views
cNMF vs LIGER
NMF
correction
batch
7 days ago by
e.r.zakiev
▴ 170
1
vote
4
replies
291
views
Analyze with Geo2R
R
NCBI
5 days ago by
anasjamshed
▴ 120
0
votes
0
replies
862
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep
sequencing
ont
nanopore
ngs
7 days ago by
Mark
• 0
0
votes
0
replies
123
views
Creating heatmap for ChIP-seq using deeptools
heatmap
chipseq
chip
deeptools
visualization
7 days ago by
biology_inform
▴ 50
0
votes
1
reply
133
views
error in plink
polygenicriskscore
prscalculation
prs
plink
error
updated 7 days ago by
biofalconch
★ 1.1k • written 7 days ago by
Emilija
• 0
0
votes
2
replies
198
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 2 days ago by
Arup Ghosh
3.2k • written 7 days ago by
vasudhapai
• 0
3
votes
2
replies
233
views
t-test by row
R
t-test
updated 7 days ago by
dthorbur
▴ 870 • written 7 days ago by
sooni
▴ 10
0
votes
0
replies
107
views
jellyfish histo is empty
jellyfish
kmer
fastq
7 days ago by
m.t.lorenc
• 0
0
votes
0
replies
120
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe
surject
vg
8 days ago by
cassiwatt
• 0
1
vote
2
replies
198
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 8 days ago by
Jeremy
▴ 840 • written 8 days ago by
camillab.
▴ 150
0
votes
1
reply
164
views
WGCNA convenience function
WGCNA
updated 7 days ago by
andres.firrincieli
3.5k • written 8 days ago by
fluentin44
• 0
0
votes
0
replies
118
views
Low mapping after Cufflinks assembly
assembly
gffread
cuffmerge
Cufflinks
RSEM
8 days ago by
sofiablancoglez
• 0
0
votes
0
replies
110
views
KEGG module and abundance of its KEGG Orthologs for functioning
function
kegg
abundance
8 days ago by
Jonathan Yoou
▴ 60
1
vote
4
replies
269
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 8 days ago by
ATpoint
78k • written 8 days ago by
annaA
▴ 10
0
votes
0
replies
112
views
RNASeq vs TermSeq
RNAseq
statistics
TermSeq
8 days ago by
npb27
• 0
0
votes
0
replies
103
views
Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?
normalization
array
8 days ago by
rk.khayami94
▴ 10
0
votes
0
replies
109
views
Interpretation of mean-variance trend in voom
EdgeR
Voom
updated 8 days ago by
Ram
41k • written 8 days ago by
Ivana
• 0
0
votes
0
replies
165
views
How to perform analysis with given copy number variation datasets between disease and control cohorts
CNV
analysis
8 days ago by
Tsin-Lau
• 0
0
votes
0
replies
111
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview
KEGG
8 days ago by
B.N.
• 0
0
votes
3
replies
268
views
Jellyfish problem with Failed to open input file 'reads.jf'
jellyfish
kmer
fastq
7 days ago by
m.t.lorenc
• 0
0
votes
6
replies
496
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4
bwa-mem
target-capture-sequencing
alignment
6 days ago by
Miguel
• 0
0
votes
0
replies
106
views
Ancestral Allele FASTA sequence aligned with Candidate Gene Region
Allele
GRSch38
Ancestral
FASTA
GRSch37
8 days ago by
Warrenkb
• 0
0
votes
3
replies
326
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 7 days ago by
MatthewP
★ 1.3k • written 8 days ago by
skinny_genes
• 0
0
votes
0
replies
143
views
Getting all the X associated genes of an organism
Rattus-norvegicus
neurobiology
updated 9 days ago by
Ram
41k • written 9 days ago by
Uri
• 0
0
votes
0
replies
121
views
coupling Cufflinks results with RSEM
transcript-level-quantification
RSEM
transcriptome-assembly
Cufflinks
9 days ago by
sofiablancoglez
• 0
4
votes
6
replies
376
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
9 days ago by
Tihana
▴ 10
2
votes
1
reply
154
views
Extract variants from 100 000 genomes project
variants
100000-genomes-project
updated 9 days ago by
Ram
41k • written 9 days ago by
Mairena
• 0
0
votes
0
replies
109
views
NA values in conumee detail
cnv
copy-number
conumee
updated 9 days ago by
Ram
41k • written 9 days ago by
sativus
▴ 10
1
vote
2
replies
256
views
How to remove batch effect in RNA-seq using control samples?
Batch-effect
RNA-seq
8 days ago by
AS20
▴ 10
0
votes
0
replies
108
views
Which of the following relationships is correct for making a hypothetical ceRNA?
cancer
lncRNA
ceRNA
RNA
miRNA
9 days ago by
mohammadhassanj
▴ 260
0
votes
0
replies
138
views
How to obtain full alignment results?
giraffe
vg
9 days ago by
nrqstudent
• 0
0
votes
1
reply
212
views
Seeking Advice on Validating RNA-Seq Data Before Differential Analysis
RNA-Seq
updated 10 days ago by
ATpoint
78k • written 10 days ago by
Tully
• 0
1
vote
1
reply
193
views
Model matrix confront 2 groups out of 3
modelmatrix
r
designformula
deseq2
drimseq
updated 10 days ago by
ATpoint
78k • written 10 days ago by
dylannicoembros
• 0
0
votes
0
replies
158
views
Extracting conserved sequences with clustralw
conservation
clustalw
updated 10 days ago by
Pierre Lindenbaum
158k • written 10 days ago by
iftikharmaryam123
• 0
1,000 results • Page
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Recent Votes
Comment: bwa mem hangs after a few thousand reads
Comment: bwa mem hangs after a few thousand reads
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
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Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
Comment: bwa mem hangs after a few thousand reads
by
cee28
▴ 30
Here is the output with the "-v 4" flag (not showing all the @SQ comments) : > @SQ SN:chrUn_GL000214v1 LN:137718 @SQ SN:chrUn_KI270742v1 L…
Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Comment: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
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