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1,160 results • Page
3 of 24
Sort: Votes
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Views
Votes
Replies
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
9 days ago by
firestar
★ 1.6k
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 10 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
12
replies
5.6k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 23 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 13 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
8
replies
464
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 1 day ago by
dariober
14k • written 4 days ago by
manaswiniparija3
▴ 40
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 9 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
13
replies
577
views
Variant calling of GBS data
GBS
variants
BQSR
21 days ago by
analyst
▴ 20
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 2 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts
DESEQ2
differential-gene-expression
kallisto
updated 9 days ago by
Ram
43k • written 2.7 years ago by
mrj
▴ 170
5
votes
3
replies
306
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax
Nextflow
Nanopore
updated 14 days ago by
colindaven
6.3k • written 15 days ago by
kerianaleerivera
• 0
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 8 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
2
replies
658
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression
RNA-Seq
DESeq2
R
updated 9 days ago by
Ram
43k • written 3.6 years ago by
ginny
• 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 2 days ago by
Ram
43k • written 3.1 years ago by
Rob
▴ 170
5
votes
14
replies
900
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 7 days ago by
GenoMax
141k • written 28 days ago by
njornet
▴ 20
5
votes
3
replies
1.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq
long-reads
normalization
short-reads
updated 16 days ago by
rpolicastro
13k • written 14 months ago by
Bernardo
▴ 20
5
votes
3
replies
361
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 7 days ago by
GenoMax
141k • written 7 days ago by
AHerik
▴ 20
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 16 days ago by
Ram
43k • written 14 months ago by
GiV17
▴ 50
5
votes
4
replies
249
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
2 days ago by
Spring
• 0
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 9 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
5
replies
833
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 6 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
5
votes
6
replies
382
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 16 days ago by
Istvan Albert
100k • written 17 days ago by
Pumla
• 0
5
votes
2
replies
307
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 15 hours ago by
shelkmike
★ 1.2k • written 23 hours ago by
kirillkirilenko
▴ 40
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 1 day ago by
Ram
43k • written 5.3 years ago by
yff
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 9 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 23 days ago by
Ram
43k • written 9.4 years ago by
galbarel
▴ 10
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 3.7 years ago by
svp
▴ 680
5
votes
3
replies
301
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 7 days ago by
cmdcolin
★ 3.8k • written 8 days ago by
William
★ 5.3k
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 2 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
5
replies
402
views
Including reference genome in SNP-based phylogeny
phylogeny
VCF
WGS
29 days ago by
maxrwjones
▴ 60
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 9 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
5
votes
5
replies
507
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 9 days ago by
joe
▴ 500 • written 10 days ago by
a615ebfb
▴ 40
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 13 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
5
votes
4
replies
516
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
11 hours ago by
BioinfGuru
★ 1.7k
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 23 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
5
votes
15
replies
4.9k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 27 days ago by
vague-barracuda-4686
• 0 • written 4.8 years ago by
Apprentice
▴ 160
5
votes
13
replies
9.0k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 7 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
5
votes
2
replies
369
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 24 days ago by
Michael
54k • written 25 days ago by
avpuzanov
• 0
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
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
4
votes
9
replies
549
views
variant calling
variant-calling
updated 15 days ago by
Ram
43k • written 16 days ago by
dalibenam64
• 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 23 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 10 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
2
replies
213
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 14 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
Lee
• 0
4
votes
5
replies
533
views
Any ways of extracting and filtering read sequences from cram files with samtools?
samtools
cram
reads
sequence
29 days ago by
sacryt
• 0
4
votes
4
replies
367
views
How do I install plink2 on a mac?
plink2
plink
updated 4 days ago by
zx8754
11k • written 6 days ago by
emilija.romic
▴ 10
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 22 days ago by
GenoMax
141k • written 13 months ago by
Andy
▴ 120
4
votes
4
replies
398
views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq
bam
20 days ago by
ntuzov
• 0
4
votes
7
replies
524
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
1,160 results • Page
3 of 24
Recent Votes
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
Answer: How to compare the quality of assemblies
Comment: How to compare the quality of assemblies
Bedtools merge but only if intersection exists
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Recent Replies
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?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
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