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352 results • Page
2 of 8
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1
vote
4
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269
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Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
16 days ago by
feather-W
• 0
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
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 3 days ago by
axol0tl
• 0 • written 6.4 years ago by
Xinwei Han
• 0
2
votes
4
replies
258
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 16 days ago by
Michael
54k • written 16 days ago by
adarsh_pp
▴ 40
0
votes
4
replies
357
views
Can I perform a Functional Enrichment Analysis on a specific list of pre-defined genes?
RNA-seq
DGE
11 days ago by
Adam
• 0
1
vote
4
replies
1.1k
views
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
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
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
300
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
20 days ago by
Aleksandr
▴ 10
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
11 hours ago by
rohitsatyam102
▴ 840
0
votes
4
replies
77
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
5 minutes ago by
BRENO
• 0
0
votes
3
replies
216
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
275
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
8 hours ago by
Nitin
• 0
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
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
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
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
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
2
votes
3
replies
240
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 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
1
vote
3
replies
272
views
RNA-seq bam file normalization
RNA-seq
bam
normalization
updated 23 days ago by
dsull
★ 5.7k • written 24 days ago by
maplewj
▴ 10
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
0
votes
3
replies
270
views
bioinformatics
bioinformatics
updated 22 days ago by
GenoMax
140k • written 22 days ago by
reachedahead225
• 0
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
1
vote
3
replies
252
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 8 days ago by
GenoMax
140k • written 8 days ago by
Sony
▴ 10
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
1
vote
3
replies
1.7k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat
sva
splicing
updated 27 days ago by
Yogi
▴ 70 • written 5.2 years ago by
ZheFrench
▴ 550
2
votes
3
replies
321
views
Spearman correlation for ATAC data
correlation
Spearman
updated 29 days ago by
gglim
▴ 140 • written 4 weeks ago by
daffodil
▴ 10
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
3
votes
3
replies
408
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 16 days ago by
Ram
43k • written 17 days ago by
Samuel
▴ 20
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
0
votes
3
replies
756
views
Corset error reading input files
corset
updated 17 days ago by
Ram
43k • written 2.3 years ago by
scarey
• 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
2
replies
332
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation
fasta
updated 8 days ago by
Dunois
★ 2.5k • written 7 weeks ago by
v.berriosfarias
▴ 140
0
votes
2
replies
239
views
How to interpret merged_calls result of command line from CNVpytor
CNVpytor
updated 18 days ago by
GenoMax
140k • written 18 days ago by
Nannapat
• 0
1
vote
2
replies
287
views
How to extract mutations in a particular gene from the VCF file of whole genome
NGS
mutations
VCF
21 days ago by
saamar.rajput
▴ 70
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
81
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
7 hours ago by
DYLAN NICO
• 0
1
vote
2
replies
220
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
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
1
vote
2
replies
238
views
Upset plot
upsetplot
10 days ago by
Chris
▴ 260
0
votes
2
replies
200
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
14 days ago by
njornet
▴ 10
0
votes
2
replies
289
views
PopGenome lost individual information
PopGenome
2 days ago by
Yixuan
• 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
173
views
RNA-seq DE with AAV injection
AAV
RNA-seq
edgeR
enrichment
updated 17 days ago by
rpolicastro
13k • written 17 days ago by
CriticalP
• 0
0
votes
2
replies
159
views
novel and know mir156 and mir172
a
updated 23 hours ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
2
votes
2
replies
212
views
ggplot2 installation
ggplot2
updated 17 days ago by
rpolicastro
13k • written 17 days ago by
safeassli
• 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
15 days ago by
Mark
• 0
352 results • Page
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Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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