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1,164 results • Page
2 of 24
Sort: replies
Rank
Views
Votes
Replies
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
6 days ago by
Ram
43k
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 8 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 27 days ago by
GenoMax
141k • written 13 months ago by
Andy
▴ 120
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 7 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
4
votes
11
replies
447
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 15 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
11
votes
11
replies
1.1k
views
7 follow
How I know if it is a batch effect or are real differences between my controls and treatments?
RNA-seq
Transcriptomics
ComBat-seq
Batch-Effect
updated 15 days ago by
GenoMax
141k • written 17 days ago by
alejandro.mejiam1
▴ 10
1
vote
11
replies
556
views
Removing adapter/primer sequence from reads while keeping flanking regions
trimming
fasta
cutadapt
BBDuk
fastq
19 days ago by
Bryan
▴ 10
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 7 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 21 hours ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 18 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 910
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 5 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
3
votes
10
replies
594
views
Piping samtools to R
R
NGS
bash
samtools
7 days ago by
joe
▴ 510
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 8 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
0
votes
10
replies
335
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
13 hours ago by
atowns21
• 0
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 7 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 7 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 14 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 6 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
8
votes
10
replies
690
views
bash script
whole-genome-sequencing
updated 8 days ago by
Ram
43k • written 16 days ago by
bestone
▴ 30
2
votes
10
replies
816
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 27 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 7 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 14 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
0
votes
10
replies
610
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
23 days ago by
dzisis1986
▴ 70
16
votes
10
replies
1.0k
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 26 days ago by
Madelaine Gogol
5.3k • written 27 days ago by
Ann
★ 2.4k
2
votes
10
replies
718
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 6 days ago by
GenoMax
141k • written 7 days ago by
me
• 0
16
votes
10
replies
7.6k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 27 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 18 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 10 days ago by
Aspire
▴ 300 • written 18 months ago by
Manav
• 0
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
28 days ago by
Zeng Jingyu
▴ 60
2
votes
9
replies
538
views
frequency of each variant per sample
freebayes
variant-frequency
updated 20 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
emilydolivo97
▴ 10
2
votes
9
replies
769
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 15 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 7 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
0
votes
9
replies
474
views
Low number of both surviving reads after trimming
trimmomatic
trimming
26 days ago by
Jay
• 0
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 7 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 7 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
4
votes
9
replies
562
views
variant calling
variant-calling
updated 21 days ago by
Ram
43k • written 22 days ago by
dalibenam64
• 0
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 11 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 6 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc
igv
updated 26 days ago by
GenoMax
141k • written 8 months ago by
huynhthienphai
• 0
0
votes
9
replies
574
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 12 days ago by
LauferVA
4.2k • written 14 days ago by
Aki
▴ 10
3
votes
9
replies
779
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 6 days ago by
Elisabeth Gasteiger
★ 2.4k • written 6 days ago by
Jacky
• 0
1
vote
9
replies
514
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
19 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 6 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
3
votes
9
replies
363
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 hours ago by
Istvan Albert
100k • written 1 day ago by
Κοσμάς
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 14 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen
cutadapt
updated 27 days ago by
Ram
43k • written 5.6 years ago by
amitpande74
▴ 20
1
vote
8
replies
677
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 15 days ago by
Anand Rao
▴ 630 • written 7 weeks ago by
bvm
▴ 20
5
votes
8
replies
2.3k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 29 days ago by
Ram
43k • written 7.7 years ago by
Amirosein
▴ 70
7
votes
8
replies
646
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 12 days ago by
spen
▴ 40 • written 15 days ago by
MBarcelo
▴ 40
1,164 results • Page
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Comment: How to convert plink files to Hapmap Format
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Sofia
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SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
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Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
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141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
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Sofia
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yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
• 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas
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GenoMax
141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed)
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▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
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Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
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Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
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Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
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