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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 28 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 8 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
1
vote
11
replies
562
views
Removing adapter/primer sequence from reads while keeping flanking regions
trimming
fasta
cutadapt
BBDuk
fastq
20 days ago by
Bryan
▴ 10
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 8 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
2
votes
10
replies
822
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 28 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 16 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 20 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 8 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
10
replies
622
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
24 days ago by
dzisis1986
▴ 70
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 7 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
16
votes
10
replies
7.7k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 29 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
3
votes
10
replies
600
views
Piping samtools to R
R
NGS
bash
samtools
8 days ago by
joe
▴ 510
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 20 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 910
1
vote
10
replies
886
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
1 day ago by
DKA
▴ 40
2
votes
10
replies
730
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 7 days ago by
GenoMax
141k • written 8 days ago by
me
• 0
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 11 days ago by
Aspire
▴ 300 • written 18 months ago by
Manav
• 0
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
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 9 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 16 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 27 days ago by
Madelaine Gogol
5.3k • written 28 days ago by
Ann
★ 2.4k
8
votes
10
replies
696
views
bash script
whole-genome-sequencing
updated 10 days ago by
Ram
43k • written 17 days ago by
bestone
▴ 30
0
votes
10
replies
400
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
2
votes
9
replies
814
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
3
votes
9
replies
790
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 7 days ago by
Elisabeth Gasteiger
★ 2.4k • written 7 days ago by
Jacky
• 0
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 7 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 8 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
0
votes
9
replies
479
views
Low number of both surviving reads after trimming
trimmomatic
trimming
27 days ago by
Jay
• 0
0
votes
9
replies
579
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 13 days ago by
LauferVA
4.2k • written 15 days ago by
Aki
▴ 10
3
votes
9
replies
407
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Istvan Albert
100k • written 3 days ago by
Κοσμάς
• 0
2
votes
9
replies
544
views
frequency of each variant per sample
freebayes
variant-frequency
updated 21 days ago by
Pierre Lindenbaum
161k • written 22 days ago by
emilydolivo97
▴ 10
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 8 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc
igv
updated 27 days ago by
GenoMax
141k • written 8 months ago by
huynhthienphai
• 0
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 12 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
29 days ago by
Zeng Jingyu
▴ 60
4
votes
9
replies
568
views
variant calling
variant-calling
updated 22 days ago by
Ram
43k • written 23 days ago by
dalibenam64
• 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
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 8 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
1
vote
9
replies
524
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
20 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
1
vote
8
replies
682
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 16 days ago by
Anand Rao
▴ 630 • written 7 weeks ago by
bvm
▴ 20
0
votes
8
replies
529
views
FreeBayes encountered a sudden error
freebayes
updated 20 days ago by
Michael
54k • written 21 days ago by
emilydolivo97
▴ 10
7
votes
8
replies
653
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 13 days ago by
spen
▴ 40 • written 16 days ago by
MBarcelo
▴ 40
7
votes
8
replies
662
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
21 days ago by
Riq
▴ 50
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 8 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen
cutadapt
updated 28 days ago by
Ram
43k • written 5.6 years ago by
amitpande74
▴ 20
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 28 days ago by
Ram
43k • written 9.9 years ago by
Kizuna
▴ 870
1
vote
8
replies
736
views
Adding CB tag to bam file
samtools
bam
updated 14 hours ago by
Pierre Lindenbaum
161k • written 7 days ago by
Maria
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 16 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1,000 results • Page
2 of 20
Recent Votes
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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Answer: Sequence read length shorter than flow cell specification
by
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The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
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Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
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Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
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Open a new question, with details.
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It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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