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
363 results • Page
4 of 8
Sort: Rank
Rank
Views
Votes
Replies
2
votes
1
reply
235
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 6 days ago by
atariw
▴ 10
4
votes
4
replies
443
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 6 days ago by
damian.szk
▴ 50 • written 7 days ago by
rohitsatyam102
▴ 840
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
Apollonia
• 0
1
vote
1
reply
234
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 6 days ago by
Ram
43k • written 6 days ago by
Fish
• 0
0
votes
0
replies
179
views
Snakemake fails to find conda in PBS
snakemake
6 days ago by
yixinzeng
• 0
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 5 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Morteza
• 0
0
votes
3
replies
297
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 6 days ago by
ATpoint
81k • written 7 days ago by
gdfsnkfns
• 0
2
votes
6
replies
492
views
Correcting coordinates in gff3 file
awk
unix
gff3
python
updated 6 days ago by
Matthias Zepper
4.5k • written 8 days ago by
hulu
• 0
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 3 days ago by
GenoMax
141k • written 14 months ago by
Estefania
▴ 30
3
votes
5
replies
442
views
Having trouble building VG in Ubuntu
vg
updated 5 days ago by
Ram
43k • written 7 days ago by
ayushm64
• 0
1
vote
3
replies
263
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 2 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
giulia.cosenza
• 0
0
votes
2
replies
256
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
7
votes
8
replies
630
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 6 days ago by
spen
▴ 40 • written 9 days ago by
MBarcelo
▴ 40
2
votes
2
replies
243
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
3 days ago by
bioinfo
▴ 150
8
votes
10
replies
658
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
0
votes
4
replies
318
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
3 days ago by
pablo
▴ 300
1
vote
10
replies
3.8k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 4 days ago by
Aspire
▴ 300 • written 18 months ago by
Manav
• 0
1
vote
3
replies
384
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 24 days ago by
Chris
▴ 260
0
votes
16
replies
1.0k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
6 days ago by
biwdpang
• 0
1
vote
1
reply
185
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
4 days ago by
CTLong
▴ 110
0
votes
2
replies
295
views
Stringtie error: Error: input file –e cannot be found!
RNA-seq
tuxedo
stringtie
transcriptomics
4 days ago by
menyawino
• 0
0
votes
2
replies
314
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 22 hours ago by
Ehsan
• 0 • written 8 weeks ago by
bioinfo
▴ 150
1
vote
2
replies
260
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
3 days ago by
bp22
▴ 60
0
votes
1
reply
190
views
Batch correction for eQTL analysis
batch
eqtl
batch-correction
batch-effect
updated 2 days ago by
Ram
43k • written 12 weeks ago by
maximal_life
▴ 20
0
votes
2
replies
515
views
autodockvina
python
python3
autodock
updated 13 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 2 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
2
votes
5
replies
985
views
Ties in reranked list
fgsea
GSEA
updated 5 days ago by
Gordon
• 0 • written 6 months ago by
Hamza
• 0
7
votes
5
replies
3.7k
views
ISCN annotation for SV/CN VCF files
SV
updated 1 day ago by
adedare
• 0 • written 7 months ago by
a.beggs
▴ 50
2
votes
2
replies
885
views
Method to detect genome doubling
CNV
genome doubling
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 4.5 years ago by
CY
▴ 750
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 2 days ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 3 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 3 days ago by
e.r.zakiev
▴ 190 • written 15 months ago by
liorglic
★ 1.4k
2
votes
3
replies
965
views
Treating "patient" as a batch effect
ComBat_seq
DESeq2
batch-Effect
updated 2 days ago by
Ram
43k • written 17 months ago by
Mia
▴ 20
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 15 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
2
votes
6
replies
848
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 2 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 3 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
1
vote
9
replies
1.1k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 23 hours ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 2 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
1
vote
2
replies
802
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 2 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 1 day ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
1
vote
3
replies
817
views
add INFO tag to vcf with bcftools
bcftools
vcf
updated 2 days ago by
Ram
43k • written 23 months ago by
from the mountains
▴ 230
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 2 hours ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 2 days ago by
Ram
43k • written 24 months ago by
mmitra
▴ 60
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 15 hours ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 15 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
2
votes
6
replies
5.1k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 15 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 2 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
363 results • Page
4 of 8
Recent Votes
Comment: Ciriquant not configuring hisat2 indexed files
Comment: Ciriquant not configuring hisat2 indexed files
DNA Methylation: Sequencing Techniques
Comment: How to install Guppy from Nanopore Technologies?
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
Recent Locations •
All
Hong Kong,
2 minutes ago
Basel, Switzerland,
2 minutes ago
China,
4 minutes ago
Pakistan,
7 minutes ago
Estonia,
7 minutes ago
Australia,
9 minutes ago
United States,
10 minutes ago
Recent Awards •
All
Popular Question
to
biwdpang
• 0
Popular Question
to
Michael
54k
Scholar
to
Gordon Smyth
★ 7.0k
Popular Question
to
yueli7
▴ 250
Popular Question
to
Chirag Parsania
★ 2.0k
Scholar
to
LChart
3.9k
Scholar
to
swbarnes2
14k
Recent Replies
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Traffic: 2714 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