Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
113 results • Page
1 of 3
Sort: replies
Rank
Views
Votes
Replies
0
votes
10
replies
338
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
15 hours ago by
atowns21
• 0
2
votes
9
replies
774
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 17 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
8
replies
270
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
2
votes
7
replies
802
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
0
votes
6
replies
421
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 9 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
1
vote
5
replies
236
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
2
votes
5
replies
673
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 4 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
2
votes
5
replies
422
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
0
votes
5
replies
252
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
7 hours ago by
njornet
▴ 20
0
votes
4
replies
491
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 days ago by
feather-W
• 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
4
replies
572
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 days ago by
Kai Xin
• 0
2
votes
4
replies
234
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
10 hours ago by
samuelkalandarov2002
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 6 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
1
vote
3
replies
224
views
some error in building kraken2 database
metagenome
kraken2
17 hours ago by
Art1ess
• 0
3
votes
3
replies
461
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
1
vote
3
replies
187
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
2
replies
530
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
0
votes
2
replies
535
views
autodockvina
python
python3
autodock
updated 5 days ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 6 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
2
replies
141
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
119
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated 5 hours ago by
Istvan Albert
100k • written 9 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
2
replies
123
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 hour ago by
swbarnes2
14k • written 14 hours ago by
Aaliya
• 0
0
votes
2
replies
365
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
1
vote
2
replies
225
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 16 days ago by
Netanel
• 0
0
votes
2
replies
183
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 10 hours ago by
b.contreras.moreira
▴ 170 • written 21 hours ago by
v.berriosfarias
▴ 140
0
votes
2
replies
407
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
0
votes
2
replies
368
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 6 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
2
replies
416
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
306
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
0
votes
2
replies
249
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 6 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
115
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 23 hours ago by
bk11
★ 2.3k • written 23 hours ago by
alphaflylizard
• 0
1
vote
1
reply
149
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
117
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
183
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 20 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
1
reply
131
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
1
reply
815
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 6 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
1
reply
258
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
1
vote
1
reply
387
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
0
votes
1
reply
120
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
1
reply
137
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
113 results • Page
1 of 3
Recent Votes
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
Answer: Fail to install umap-learn in R
Answer: Fail to install umap-learn in R
What are Tiles in Sequencing
Recent Locations •
All
United States,
6 minutes ago
Finland,
6 minutes ago
Canada,
8 minutes ago
United Kingdom,
9 minutes ago
United States,
10 minutes ago
United States,
11 minutes ago
Poland,
12 minutes ago
Recent Awards •
All
Popular Question
to
Russ
▴ 500
Popular Question
to
camillab.
▴ 160
Popular Question
to
pramach1
▴ 40
Popular Question
to
Adyasha
• 0
Popular Question
to
sehriban.buyukkilic
▴ 10
Popular Question
to
O.rka
▴ 710
Popular Question
to
Akash D
▴ 40
Recent Replies
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
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
by
Maria
• 0
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
by
haibol2017
▴ 10
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…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
by
swbarnes2
14k
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…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
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…
Comment: AGeNT LocatIt
by
barslmn
★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
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
by
Sofia
• 0
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
by
GenoMax
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
by
Sofia
• 0
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…
Traffic: 2553 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6