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933 results • Page
1 of 19
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76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
15 days ago by
Kevin Blighe
87k
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 23 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 7 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 10 days ago by
i.sudbery
19k • written 12 days ago by
noodle
▴ 580
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 22 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 22 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 23 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 28 days ago by
e.r.zakiev
▴ 210 • written 4.3 years ago by
kevin.stachelek
▴ 80
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 21 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 23 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 13 days ago by
bk11
★ 2.4k • written 9 weeks ago by
Sofia
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 3 days ago by
Pierre Lindenbaum
161k • written 5.7 years ago by
mostafarafiepour
▴ 180
7
votes
16
replies
779
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
11 days ago by
Ruqaiya
• 0
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
27 days ago by
biwdpang
• 0
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 21 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 6 days ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
13
votes
14
replies
812
views
High Malat-1 expression in single cell data
single-cell
updated 2 days ago by
t.montserrat.ayuso
▴ 40 • written 11 days ago by
carolofharvest
▴ 40
10
votes
14
replies
664
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 2 days ago by
GenoMax
142k • written 8 days ago by
nicole.kavanagh
• 0
5
votes
14
replies
1.1k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 29 days ago by
GenoMax
142k • written 7 weeks ago by
njornet
▴ 20
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 7 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
4
votes
13
replies
971
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 23 days ago by
BioinfGuru
★ 1.7k • written 28 days ago by
matteo.levorato
• 0
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 16 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
5
votes
13
replies
1.7k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 19 days ago by
ATpoint
82k • written 21 days ago by
BioinfGuru
★ 1.7k
5
votes
13
replies
9.3k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 29 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 24 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 22 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
22 days ago by
Ram
43k
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 7 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 22 hours ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 21 days ago by
Ram
43k • written 21 days ago by
iamsmor
• 0
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 21 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 4 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 13 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
0
votes
11
replies
677
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
14 days ago by
atowns21
• 0
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 23 days ago by
Ram
43k • written 6.5 years ago by
shania90.lk
▴ 30
4
votes
11
replies
845
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 16 days ago by
LauferVA
4.2k • written 17 days ago by
dominickd
• 0
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 23 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 16 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
2
votes
11
replies
953
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 11 days ago by
jkbonfield
★ 1.2k • written 22 days ago by
me
• 0
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 23 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
8
votes
10
replies
792
views
bash script
whole-genome-sequencing
updated 24 days ago by
Ram
43k • written 4 weeks ago by
bestone
▴ 30
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 21 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 23 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
1
vote
10
replies
860
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 4 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
15 days ago by
DKA
▴ 40
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 22 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 23 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 26 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
0
votes
10
replies
573
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 10 days ago by
i.sudbery
19k • written 17 days ago by
Patadu94
• 0
933 results • Page
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Recent Votes
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
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Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
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Comment: samtools tview symbols
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What does the star mean then ?
Comment: RNA seq analysis
by
prifa
▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
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by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
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Giulia
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The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
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manaswwm
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If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list
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★ 1.8k
I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
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