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1,000 results • Page
2 of 20
Sort: replies
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Views
Votes
Replies
11
votes
12
replies
931
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 5 days ago by
Ram
43k • written 6 days ago by
iamsmor
• 0
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 1 day ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
1
vote
11
replies
557
views
Removing adapter/primer sequence from reads while keeping flanking regions
trimming
fasta
cutadapt
BBDuk
fastq
19 days ago by
Bryan
▴ 10
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 18 days ago by
alejandro.mejiam1
▴ 10
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
454
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 18 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
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
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
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
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
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 15 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
3
votes
10
replies
595
views
Piping samtools to R
R
NGS
bash
samtools
7 days ago by
joe
▴ 510
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
8
votes
10
replies
692
views
bash script
whole-genome-sequencing
updated 8 days ago by
Ram
43k • written 16 days ago by
bestone
▴ 30
0
votes
10
replies
614
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
23 days ago by
dzisis1986
▴ 70
16
votes
10
replies
7.6k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 28 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
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 6 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 7 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 19 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 910
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 9 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 15 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
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
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 19 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
0
votes
10
replies
341
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
16 hours ago by
atowns21
• 0
1
vote
10
replies
752
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
22 minutes ago by
DKA
▴ 40
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
2
votes
10
replies
720
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
2
votes
10
replies
819
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
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
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
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
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
2
votes
9
replies
776
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 18 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
4
votes
9
replies
563
views
variant calling
variant-calling
updated 21 days ago by
Ram
43k • written 22 days ago by
dalibenam64
• 0
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
0
votes
9
replies
576
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
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
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
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
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 7 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
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
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
3
votes
9
replies
376
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 6 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 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
0
votes
9
replies
475
views
Low number of both surviving reads after trimming
trimmomatic
trimming
26 days ago by
Jay
• 0
3
votes
9
replies
782
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
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 21 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
0
votes
8
replies
522
views
FreeBayes encountered a sudden error
freebayes
updated 19 days ago by
Michael
54k • written 20 days ago by
emilydolivo97
▴ 10
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
1,000 results • Page
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Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Answer: Fail to install umap-learn in R
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Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
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It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
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Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
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@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
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Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
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We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
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Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
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RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
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He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
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