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351 results • Page
2 of 8
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1
vote
4
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1.1k
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NGS/GATK pipeline returns too many variants
NGS
WES
GATK
Mutect
updated 9 days ago by
dhruti
• 0 • written 3.1 years ago by
dodausp
▴ 180
0
votes
4
replies
1.7k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing
illumina
updated 28 days ago by
charbelelias30
• 0 • written 3.3 years ago by
WhiteN8
• 0
1
vote
4
replies
267
views
Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
16 days ago by
feather-W
• 0
0
votes
4
replies
241
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
5 hours ago by
rohitsatyam102
▴ 840
0
votes
4
replies
330
views
PCA Plot in Single-cell RNA-seq Data
RNA-seq
PCA
single
cell
29 days ago by
Darya
• 0
3
votes
4
replies
299
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
19 days ago by
Aleksandr
▴ 10
1
vote
4
replies
300
views
Differential analysis using R
DNA
methylation
updated 23 days ago by
Michael
54k • written 23 days ago by
maryak
▴ 20
3
votes
4
replies
426
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq
Chip-Seq
ATAC-Seq
29 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
336
views
Dsuite Dinvestigate error but no indication as to the source
Dsuite
20 days ago by
Drew
• 0
2
votes
4
replies
257
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 16 days ago by
Michael
54k • written 16 days ago by
adarsh_pp
▴ 40
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
0
votes
3
replies
225
views
Microarray pbrobe ID to gene ID problem
microarray
updated 13 days ago by
GenoMax
140k • written 14 days ago by
mnx0723
• 0
2
votes
3
replies
320
views
Spearman correlation for ATAC data
correlation
Spearman
updated 29 days ago by
gglim
▴ 140 • written 4 weeks ago by
daffodil
▴ 10
0
votes
3
replies
215
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
2 hours ago by
Nitin
• 0
0
votes
3
replies
298
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
6 days ago by
kabir.deb
▴ 80
0
votes
3
replies
211
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
0
votes
3
replies
674
views
PCR duplicates in FFPE RNASeq
PCR-duplicates
RNA-Seq
FFPE
Variant-Calling
updated 2 days ago by
Ram
43k • written 21 months ago by
Gama313
▴ 120
1
vote
3
replies
287
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 16 days ago by
GenoMax
140k • written 16 days ago by
Matt
• 0
1
vote
3
replies
252
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 7 days ago by
GenoMax
140k • written 8 days ago by
Sony
▴ 10
1
vote
3
replies
272
views
RNA-seq bam file normalization
RNA-seq
bam
normalization
updated 22 days ago by
dsull
★ 5.7k • written 24 days ago by
maplewj
▴ 10
0
votes
3
replies
240
views
data background noise
noise
data
updated 8 days ago by
dthorbur
★ 1.7k • written 14 days ago by
marco.barr
▴ 30
1
vote
3
replies
232
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions
prediction
deeplearning
updated 10 days ago by
dthorbur
★ 1.7k • written 14 days ago by
Alex
• 0
2
votes
3
replies
427
views
Genes with multiple chromosome locations
gene
annotation
loci
alternative
updated 24 days ago by
Alex Reynolds
35k • written 26 days ago by
Pac314
▴ 10
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap
psmc
updated 3 days ago by
xuby963
• 0 • written 3.1 years ago by
truebeliever24
▴ 50
5
votes
3
replies
287
views
samtools view: error reading file
samtools
bowtie2
updated 22 days ago by
bioinfo_ga
▴ 70 • written 24 days ago by
ray
• 0
0
votes
3
replies
756
views
Corset error reading input files
corset
updated 16 days ago by
Ram
43k • written 2.3 years ago by
scarey
• 0
0
votes
3
replies
333
views
Tools and software to visualize the moving cell compartments in 3D
3D-visualization
cell-compartments
20 days ago by
saamar.rajput
▴ 70
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral
genome
updated 20 days ago by
illodukarthickbabu
• 0 • written 2.6 years ago by
alslonik
▴ 310
3
votes
3
replies
407
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 15 days ago by
Ram
43k • written 17 days ago by
Samuel
▴ 20
0
votes
3
replies
270
views
bioinformatics
bioinformatics
updated 21 days ago by
GenoMax
140k • written 21 days ago by
reachedahead225
• 0
2
votes
3
replies
238
views
Extracting information from my VCF file
VCF
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
2
votes
3
replies
781
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
updated 20 days ago by
Amy
▴ 20 • written 22 months ago by
desicasares
▴ 40
1
vote
3
replies
254
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 9 days ago by
dsull
★ 5.7k • written 10 days ago by
newuser2024
• 0
1
vote
3
replies
1.7k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat
sva
splicing
updated 26 days ago by
Yogi
▴ 70 • written 5.2 years ago by
ZheFrench
▴ 550
0
votes
2
replies
305
views
BMI as a continuous variable is my outcome, which type data i should put to calculate
transcriptomics
29 days ago by
jiefei
• 0
0
votes
2
replies
218
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
2 days ago by
eesiribloom
▴ 50
0
votes
2
replies
173
views
RNA-seq DE with AAV injection
AAV
RNA-seq
edgeR
enrichment
updated 16 days ago by
rpolicastro
13k • written 17 days ago by
CriticalP
• 0
1
vote
2
replies
219
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
1
vote
2
replies
238
views
Upset plot
upsetplot
10 days ago by
Chris
▴ 260
2
votes
2
replies
212
views
ggplot2 installation
ggplot2
updated 16 days ago by
rpolicastro
13k • written 16 days ago by
safeassli
• 0
0
votes
2
replies
1.3k
views
Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNA-seq
RNA-Seq
SoupX
updated 9 days ago by
e.r.zakiev
▴ 170 • written 3.4 years ago by
AA
• 0
0
votes
2
replies
229
views
Problem merging plink files for somatic variants.
plink
somatic
vcf
18 days ago by
Palgrave
▴ 110
0
votes
2
replies
149
views
novel and know mir156 and mir172
a
updated 17 hours ago by
gayachit
▴ 200 • written 20 hours ago by
Fadmo
• 0
2
votes
2
replies
207
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
3
votes
2
replies
271
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Annotation
Single
Bioinformatics
Cell
27 days ago by
Daddy
▴ 20
2
votes
2
replies
73
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 1 hour ago by
dariober
14k • written 6 hours ago by
Pumla
• 0
0
votes
2
replies
288
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
0
votes
2
replies
72
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 1 hour ago by
Ram
43k • written 5 hours ago by
gdfsnkfns
• 0
2
votes
2
replies
262
views
compare dimplot(single cell)
DEG
scRNAseq
12 days ago by
kayah
• 0
0
votes
2
replies
202
views
Is there a program that can predict the sequence of an organisms telomeres just from raw sequencing reads
telomeres
genomics
sequencing
14 days ago by
Mark
• 0
351 results • Page
2 of 8
Recent Votes
Which human reference genome should I use?
Comment: Centromere and telomere positions for Chm13v2 assembly
C: Last column in UCSC cytoBands.txt files
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
Comment: Gene reads all zero for each sample
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Looks like those appear to be "polycomb associated non-coding RNA". You probably know what they are. https://www.ncbi.nlm.nih.gov/nuccore/…
Comment: Parsing fasta file by coordinates
by
GenoMax
140k
> sequences that are from the same region from those that aren't. could refer to sequence composition and that is the reason we were sugge…
Comment: Low number of both surviving reads after trimming
by
Ram
43k
Please edit your post and add the code parts again, this time use the `101010` code button and NOT the double quote button. The latter is u…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Pierre Lindenbaum
160k
... reminds me [https://twitter.com/yokofakun/status/1267877851795259397][1] ( my twitter account is now private) ![ops][2] [1]: https…
Comment: Flow Cytometry Data Analysis by Seurat
by
Ram
43k
Why did you delete this post, https://www.biostars.org/u/142036/ ?
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
dariober
14k
Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
ATpoint
81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
Answer: ONT direct RNA sequencing
by
joe
▴ 470
You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
★ 1.1k
You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
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