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93 results • Page
2 of 2
Sort: Views
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Views
Votes
Replies
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 17 hours ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
0
votes
1
reply
804
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 17 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
724
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 17 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
11
votes
12
replies
704
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 13 hours ago by
Ram
43k • written 18 hours ago by
iamsmor
• 0
2
votes
7
replies
688
views
Removing duplicates
duplicates
ONT
minimap2
updated 12 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
1
vote
9
replies
630
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 22 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 1 day ago by
Jacky
• 0
2
votes
10
replies
603
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
1
vote
4
replies
587
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 20 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
5
votes
4
replies
533
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
15 hours ago by
BioinfGuru
★ 1.7k
0
votes
2
replies
516
views
autodockvina
python
python3
autodock
updated 14 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
4
replies
451
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 hours ago by
Kai Xin
• 0
3
votes
4
replies
379
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
n_navy
• 0
0
votes
1
reply
377
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 21 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
3
votes
3
replies
362
views
Korean human genome reference file
GWAS
reference
imputation
7 hours ago by
SeoGyun
• 0
2
votes
3
replies
361
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
22 hours ago by
valentinatsar
• 0
0
votes
2
replies
353
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
10 hours ago by
航太郎
• 0
3
votes
4
replies
351
views
biomaRt error for different R version
biomaRt
R
updated 23 hours ago by
GenoMax
141k • written 2 days ago by
manaswwm
▴ 490
2
votes
2
replies
344
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
19 hours ago by
nhaus
▴ 300
0
votes
3
replies
339
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 12 hours ago by
swbarnes2
14k • written 1 day ago by
rrehimi
• 0
5
votes
2
replies
324
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 19 hours ago by
shelkmike
★ 1.2k • written 1 day ago by
kirillkirilenko
▴ 40
0
votes
2
replies
314
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 23 hours ago by
Ehsan
• 0 • written 8 weeks ago by
bioinfo
▴ 150
0
votes
1
reply
253
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 10 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
2
votes
2
replies
251
views
Ciriquant not configuring hisat2 indexed files
ciriquant
1 hour ago by
Atul K.
• 0
1
vote
1
reply
245
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
20 hours ago by
otieno43
▴ 30
0
votes
2
replies
238
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 hours ago by
Ashok
• 0
1
vote
2
replies
228
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 3 hours ago by
Pierre Lindenbaum
161k • written 14 hours ago by
rahu
• 0
0
votes
2
replies
223
views
python file for coding potential calculator
cpc2.py
7 hours ago by
Ashok
• 0
0
votes
2
replies
216
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
7 hours ago by
Ashok
• 0
0
votes
1
reply
203
views
DEseq2
RNA-seq
DESeq2
updated 21 hours ago by
Ram
43k • written 1 day ago by
rrehimi
• 0
0
votes
2
replies
200
views
Adding CB tag to bam file
samtools
bam
2 hours ago by
Maria
• 0
0
votes
1
reply
187
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
predeus
★ 1.9k
0
votes
1
reply
170
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 19 hours ago by
Ram
43k • written 20 hours ago by
_quantum_girl_
▴ 10
2
votes
1
reply
123
views
Free/open source 23andme-like analysis
NGS
SNPs
genomics
VCF
updated 2 hours ago by
Michael
54k • written 7 hours ago by
joe
▴ 510
0
votes
0
replies
105
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 20 hours ago by
Ram
43k • written 1 day ago by
bioinfo223
▴ 10
0
votes
0
replies
103
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 21 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
100
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 20 hours ago by
Ram
43k • written 22 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
99
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 20 hours ago by
Ram
43k • written 20 hours ago by
Javier
• 0
0
votes
0
replies
98
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
16 hours ago by
Chris
▴ 260
0
votes
0
replies
91
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 19 hours ago by
Ram
43k • written 19 hours ago by
samuelkalandarov2002
• 0
0
votes
0
replies
90
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
20 hours ago by
enferdeflame
• 0
0
votes
0
replies
84
views
create genewise sync file in popoolation
popoolation
updated 14 hours ago by
GenoMax
141k • written 15 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
0
replies
53
views
Lncipedia GTF file error
Proteomics
Bioinformatics
4 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
23
views
miRDeep2: How to get the read counts
mirdeep2
1 hour ago by
Atul K.
• 0
93 results • Page
2 of 2
Recent Votes
A: Counting Number Of Bases In A Fastq File
Free/open source 23andme-like analysis
Comment: Free/open source 23andme-like analysis
Answer: Missing protein (VEGF-A) in String db
Answer: Missing protein (VEGF-A) in String db
Answer: Ciriquant not configuring hisat2 indexed files
Answer: Ciriquant not configuring hisat2 indexed files
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Popular Question
to
i.sudbery
19k
Popular Question
to
biwdpang
• 0
Popular Question
to
Michael
54k
Scholar
to
Gordon Smyth
★ 7.0k
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yueli7
▴ 250
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★ 2.0k
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LChart
3.9k
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
▴ 510
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?
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