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177 results • Page
3 of 4
Sort: Votes
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Votes
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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
3
replies
267
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
5 days ago by
Sara
▴ 230
0
votes
0
replies
155
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
5 days ago by
kdca
• 0
0
votes
0
replies
155
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
5 days ago by
bioinfo
▴ 60
0
votes
3
replies
299
views
Annovar - Annotated file cells show string
annovar
5 days ago by
Roshan
• 0
0
votes
0
replies
223
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
5 days ago by
Wenke
• 0
0
votes
1
reply
236
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 4 days ago by
GenoMax
136k • written 5 days ago by
Soumajit
▴ 40
0
votes
0
replies
167
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
4 days ago by
rohitsatyam102
▴ 780
0
votes
3
replies
332
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 4 days ago by
ATpoint
78k • written 5 days ago by
manuelmourato25
• 0
0
votes
1
reply
236
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 4 days ago by
GenoMax
136k • written 4 days ago by
subhiksha
• 0
0
votes
3
replies
304
views
subset a bam file
bam
pysam
NGS
samtools
updated 4 days ago by
GenoMax
136k • written 4 days ago by
Ming
• 0
0
votes
2
replies
260
views
Use of IDR after running MACS3 for ATAC-seq data
ATAC-seq
MACS2
MACS3
3 days ago by
Orange
▴ 10
0
votes
3
replies
360
views
Extracting list of identical items from several excel files
from
excel
items
Extract
file
updated 3 days ago by
DonPhager
• 0 • written 4 days ago by
otieno43
▴ 20
0
votes
0
replies
117
views
Negative F statistics for sex check in plink
plink
check
sex
3 days ago by
kl
▴ 10
0
votes
0
replies
104
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
3 days ago by
jiazheng_lin
• 0
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 2 days ago by
Cibo
• 0 • written 2.0 years ago by
Amina
• 0
0
votes
7
replies
323
views
snp database using annotation
database
gwas
snp
annotation
2 days ago by
sskimvd
• 0
0
votes
0
replies
95
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
2 days ago by
Jaykishan
• 0
0
votes
7
replies
415
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
2 days ago by
Foad
▴ 10
0
votes
0
replies
87
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
2 days ago by
user230613
▴ 350
0
votes
1
reply
173
views
multiple condition and time course in RNA-seq
edgeR
RNA-Seq
DESeq2
updated 2 days ago by
i.sudbery
18k • written 3 days ago by
tiancaigg
▴ 30
0
votes
2
replies
683
views
CPAT: error on coding probability cutoff
lncRNA
RNAseq
CPAT
updated 2 days ago by
catarinaventura_pt
• 0 • written 21 months ago by
xiaoxia8923
• 0
0
votes
2
replies
184
views
RnBeads mean difference vs M-values
Methylation
updated 2 days ago by
Basti
★ 1.8k • written 3 days ago by
a.basitkhan1990
▴ 30
0
votes
1
reply
151
views
Combine Geoids
Geoids
NCBI
updated 2 days ago by
ATpoint
78k • written 2 days ago by
anasjamshed
▴ 120
0
votes
4
replies
239
views
Species coverage in the NCBI protein NR database ?
NR
updated 2 days ago by
Istvan Albert
99k • written 2 days ago by
HERMAN
▴ 10
0
votes
4
replies
234
views
HTseq reports missing attribute name
htseq
2 days ago by
Bjorn
• 0
0
votes
1
reply
186
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 2 days ago by
Arup Ghosh
3.2k • written 3 days ago by
Mehwish
▴ 10
0
votes
2
replies
199
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
0
votes
1
reply
241
views
Diferences between TCGAbiolinks and cBioportal
R
TCGAbiolinks
cBioportal
updated 2 days ago by
Zhenyu Zhang
★ 1.1k • written 6 days ago by
jomagrax
▴ 40
0
votes
2
replies
211
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
2 days ago by
jen
• 0
0
votes
0
replies
321
views
Job:
Postdoctoral Researcher in Alzheimer's disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA
Multi-Omics
Imaging
Alzheimer
Genetics
1 day ago by
belloy
• 0
0
votes
3
replies
3.9k
views
pheatmap lengends are being cutoff
pheatmap
legends
rstudio
heatmaps
updated 1 day ago by
Chris S.
▴ 320 • written 2.7 years ago by
enh
• 0
0
votes
0
replies
100
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
0
votes
0
replies
85
views
String App in Cytoscape
App
String
cytoscape
1 day ago by
hellokwmin
• 0
0
votes
5
replies
527
views
Lack of correspondance of GFA node IDs to giraffe/call node IDs
giraffe
pggb
vg
updated 1 day ago by
Wenhai
• 0 • written 6 weeks ago by
javierbelmor
• 0
0
votes
3
replies
215
views
merged rs number information
merged
dbsnp
1 day ago by
sskimvd
• 0
0
votes
4
replies
164
views
MRI VBM issue
MRI
VBM
ROI
Rhesus
1 day ago by
Ethan Lee
• 0
0
votes
0
replies
93
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
1 day ago by
Smriti
▴ 10
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
6
replies
263
views
I made an error when using metawrap to binning
metagenome
binning
metawrap
1 day ago by
alice005201314
• 0
0
votes
1
reply
135
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
Saurabh
• 0
0
votes
1
reply
135
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 1 day ago by
GenoMax
136k • written 1 day ago by
praasu
▴ 40
0
votes
0
replies
81
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
1 day ago by
rbronste
▴ 420
0
votes
1
reply
113
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 1 day ago by
singh.vijender
▴ 100 • written 1 day ago by
reza
▴ 300
0
votes
3
replies
283
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 1 day ago by
jv
★ 1.2k • written 7 days ago by
TC_Chang
▴ 10
0
votes
2
replies
181
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
1 day ago by
harter-ainsworth.izaak
• 0
0
votes
0
replies
113
views
Bcftools consensus when reference is a deletion
consensus
vcf
1 day ago by
selplat21
▴ 20
0
votes
1
reply
122
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 1 day ago by
ATpoint
78k • written 1 day ago by
ahonya
• 0
0
votes
2
replies
308
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 21 hours ago by
cmdcolin
★ 3.4k • written 22 hours ago by
Dylan C-C
• 0
0
votes
0
replies
72
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
19 hours ago by
Richard Fontaine
• 0
177 results • Page
3 of 4
Recent Votes
Comment: Merging several vcf files for GWAS?
Comment: p-value combination methods
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
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Comment: Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
by
ian.will
▴ 10
Yep gave that a go and proceeding with the analysis. Thanks again.
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
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