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1,000 results • Page
3 of 20
Sort: Votes
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Views
Votes
Replies
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 19 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 15 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 14 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
8
replies
2.3k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 29 days ago by
Ram
43k • written 7.7 years ago by
Amirosein
▴ 70
5
votes
3
replies
701
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 5 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
4
replies
616
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
6 days ago by
BioinfGuru
★ 1.7k
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 8 days ago by
Ram
43k • written 3.8 years ago by
svp
▴ 680
5
votes
4
replies
302
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
8 days ago by
Spring
• 0
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 22 days ago by
rpolicastro
13k • written 15 months ago by
Bernardo
▴ 20
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 8 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
5
replies
535
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 15 days ago by
joe
▴ 510 • written 16 days ago by
a615ebfb
▴ 40
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 7 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
5
replies
844
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 12 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
5
votes
14
replies
952
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 13 days ago by
GenoMax
141k • written 4 weeks ago by
njornet
▴ 20
5
votes
3
replies
316
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 12 days ago by
cmdcolin
★ 3.8k • written 14 days ago by
William
★ 5.3k
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 22 days ago by
Ram
43k • written 14 months ago by
GiV17
▴ 50
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 days ago by
ATpoint
82k • written 5 days ago by
BioinfGuru
★ 1.7k
5
votes
3
replies
316
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax
Nextflow
Nanopore
updated 20 days ago by
colindaven
6.4k • written 21 days ago by
kerianaleerivera
• 0
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 7 days ago by
Ram
43k • written 5.3 years ago by
yff
• 0
5
votes
2
replies
662
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression
RNA-Seq
DESeq2
R
updated 15 days ago by
Ram
43k • written 3.6 years ago by
ginny
• 0
5
votes
13
replies
9.1k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 13 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
5
votes
3
replies
384
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 13 days ago by
GenoMax
141k • written 13 days ago by
AHerik
▴ 20
5
votes
4
replies
610
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
19 hours ago by
kirillkirilenko
▴ 40
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days 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 8 days ago by
hamarillo
▴ 70 • written 5.7 years ago by
silviajserrano
▴ 50
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 29 days ago by
Ram
43k • written 9.4 years ago by
galbarel
▴ 10
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 15 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 15 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
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 15 days ago by
Ram
43k • written 2.7 years ago by
mrj
▴ 170
5
votes
6
replies
390
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 22 days ago by
Istvan Albert
100k • written 23 days ago by
Pumla
• 0
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 26 days ago by
Ram
43k • written 8.1 years ago by
nikelle.petrillo
▴ 110
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 19 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
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 29 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
4
replies
462
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 12 days ago by
damian.szk
▴ 70 • written 13 days ago by
rohitsatyam102
▴ 840
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 15 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 27 days ago by
GenoMax
141k • written 13 months ago by
Andy
▴ 120
4
votes
13
replies
851
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 7 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
matteo.levorato
• 0
4
votes
2
replies
221
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 20 days ago by
Pierre Lindenbaum
161k • written 20 days ago by
Lee
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 7 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
4
votes
4
replies
327
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
15 days ago by
Morteza
• 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 7 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 15 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
4
votes
4
replies
457
views
Error Codes in Snakemake
python
snakemake
19 days ago by
888pea
▴ 10
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc
igv
updated 27 days ago by
GenoMax
141k • written 8 months ago by
huynhthienphai
• 0
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 22 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
4
votes
4
replies
404
views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq
bam
26 days ago by
ntuzov
• 0
4
votes
6
replies
442
views
Odd results with BLAST remote
blast
remote
NCBI
updated 8 days ago by
b.contreras.moreira
▴ 170 • written 9 days ago by
Begonia_pavonina
▴ 150
4
votes
3
replies
1.3k
views
GATK best practices for Broad-produced NGS data
NGS
GATK4
BroadInstitute
Variant-Calling
updated 29 days ago by
Ram
43k • written 5.4 years ago by
Mehulsharma.253
▴ 30
1,000 results • Page
3 of 20
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Answer: clustalo - align milions of short seq, memory issue
by
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▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
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161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
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Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
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by
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14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
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14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
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• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
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▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
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by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
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by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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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…
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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…
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