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1,000 results • Page
3 of 20
Sort: Views
Rank
Views
Votes
Replies
2
votes
8
replies
2.9k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 11 months ago by
Ram
43k • written 7.1 years ago by
AJTrunkskun94
• 0
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 7 months ago by
Ram
43k • written 5.8 years ago by
AP
▴ 80
1
vote
3
replies
2.8k
views
Multiple Sequence Alignment Python
multiple-sequence-alignment
ClustalW
Biopython
updated 11 months ago by
Ram
43k • written 6.0 years ago by
Manu Madhavan
▴ 20
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 8.5 years ago by
annadv
• 0
1
vote
1
reply
2.8k
views
Comparing time series expression data
time-series
gene-expression
updated 10 months ago by
Ram
43k • written 6.7 years ago by
The
▴ 180
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 1 day ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
3
replies
2.8k
views
Circos plot for ecoli genome
rna-seq
circos
updated 7 months ago by
Ram
43k • written 7.4 years ago by
raya.girish
▴ 30
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
3
replies
2.8k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 10 months ago by
Ram
43k • written 4.6 years ago by
marquezg48
• 0
0
votes
4
replies
2.8k
views
Music Tool Integration To Galaxy Ngs
music
galaxy
updated 9 months ago by
Ram
43k • written 10.1 years ago by
Chetan Joshi
▴ 20
1
vote
1
reply
2.8k
views
Hmmer Alignment input parse error
alignment
hmmer
updated 11 months ago by
Ram
43k • written 6.8 years ago by
hivemind
▴ 20
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
5
replies
2.7k
views
Visualize VarScan2 Copy Number Aberrations in IGV
VarScan2
sequence
alignment
IGV
updated 9 months ago by
Ram
43k • written 8.0 years ago by
plumgwodehouse
• 0
3
votes
3
replies
2.7k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 6 months ago by
Ram
43k • written 2.6 years ago by
Anand
▴ 40
0
votes
0
replies
2.7k
views
Are secondary alignments (SAM) produced by STAR aligner linked with MAPQ score?
alignment
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Claudio
• 0
0
votes
2
replies
2.7k
views
How to get Haplotype file from PLINK format data
SNP
PLINK
updated 11 months ago by
Ram
43k • written 6.0 years ago by
bha
▴ 80
0
votes
1
reply
2.7k
views
how to read h5 file in Seurat if its structure is not like 10x h5 file structure?
RNA-Seq
single-cell
scRNA-seq
Seurat
R
updated 7 months ago by
Ram
43k • written 2.3 years ago by
fifty_fifty
▴ 60
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 25 days ago by
axol0tl
• 0 • written 6.5 years ago by
Xinwei Han
• 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
2
votes
3
replies
2.7k
views
Merge really large amount of Seurat objects
Seurat
9 months ago by
Andy
▴ 120
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 10 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
1
vote
3
replies
2.7k
views
g++: error:unrecognized command line option ‘-std=c++2a’
gcc
updated 11 months ago by
Rob
6.5k • written 11 months ago by
wangjincheng
• 0
0
votes
0
replies
2.7k
views
GROMACS RMSD COMMANDS
gromacs
updated 9 months ago by
Ram
43k • written 8.3 years ago by
adammbbs
▴ 10
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 2 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
1
vote
1
reply
2.7k
views
trinity assembly error, run failed
trinity
rna-seq
updated 7 months ago by
Ram
43k • written 7.9 years ago by
nikelle.petrillo
▴ 110
1
vote
5
replies
2.7k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 10 months ago by
Ram
43k • written 6.1 years ago by
zizigolu
★ 4.3k
4
votes
7
replies
2.6k
views
low bootstrap value?
phylogeny
genome
alignment
updated 10 months ago by
Ram
43k • written 4.8 years ago by
Kumar
▴ 120
4
votes
14
replies
2.6k
views
Is it possible to annotate single genes by snpeff
snp
vcf
updated 9 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
0
votes
1
reply
2.6k
views
get counts by gene for single cell rna seq
scRNA-seq
single-cell
updated 10 months ago by
Ram
43k • written 3.1 years ago by
das2000sidd
▴ 30
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 10 days ago by
Ram
43k • written 8.0 years ago by
Chris Gene
▴ 80
0
votes
0
replies
2.6k
views
monocle clustering cells without marker genes error
R
RNA-Seq
monocle
updated 10 months ago by
Ram
43k • written 5.7 years ago by
hsu
▴ 40
1
vote
0
replies
2.6k
views
Running Multiple Alignments in MEGA with a script produces errors.
next-gen
RNA-Seq
MEGA
multiple-alignment
updated 11 months ago by
Ram
43k • written 8.1 years ago by
rachelrodgers12
▴ 10
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 9 months ago by
GenoMax
141k • written 2.3 years ago by
Komalharini
• 0
1
vote
4
replies
2.6k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 11 months ago by
Ram
43k • written 8.0 years ago by
nchuang
▴ 260
0
votes
7
replies
2.6k
views
How to perform gene annotation in kallisto?
Gene
kallisto
annotation
updated 7 months ago by
호성
• 0 • written 2.6 years ago by
synat.keam
▴ 100
0
votes
3
replies
2.6k
views
Picard's Tool MarkDuplicates problem
picard
updated 10 months ago by
Ram
43k • written 4.2 years ago by
harmadikemil
• 0
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
11 months ago by
Sowmya Pulapet
▴ 70
3
votes
7
replies
2.5k
views
6 follow
Online BLAST search using R
BLAST
R
updated 9 weeks ago by
SequenceServer
▴ 140 • written 2.7 years ago by
accibio
▴ 20
0
votes
3
replies
2.5k
views
PLINK can't find my files?
software-error
plink
windows
SNP
updated 4 months ago by
irene.treccani.work
• 0 • written 7.5 years ago by
stephanie.langevin
• 0
0
votes
4
replies
2.5k
views
picard markduplicate output smaller file
picard
markduplicates
gatk
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Peter Chung
▴ 200
0
votes
6
replies
2.5k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 10 months ago by
Ram
43k • written 3.9 years ago by
yaoyao20152031
• 0
0
votes
3
replies
2.5k
views
Create small BAM file with pysam and iterate over reads
samtools
bam
pysam
updated 9 months ago by
Ram
43k • written 6.5 years ago by
lebedana21
• 0
2
votes
1
reply
2.5k
views
Converting blastn output to VCF (for SNPs): what is the quickest way?
VCF
blast
SNP
xml
updated 9 months ago by
Ram
43k • written 6.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.5k
views
problem with updating trinity
software-error
trinity
updated 10 months ago by
Ram
43k • written 5.4 years ago by
ashokkumar.mb
• 0
1
vote
4
replies
2.5k
views
MesKit error message - Join columns must be present in data.
MesKit
R
updated 9 months ago by
bataibence
• 0 • written 14 months ago by
CH1374
▴ 10
0
votes
0
replies
2.5k
views
Analysis and tools for gene/pathway conservation
evolution
updated 10 months ago by
Ram
43k • written 9.0 years ago by
hbw
▴ 90
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.8 years ago by
zorn21g
• 0
0
votes
2
replies
2.4k
views
Error while running MEGAX
multiple-sequence-alignment
MEGAX
updated 11 months ago by
Ram
43k • written 5.9 years ago by
Mohak
▴ 20
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 5 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
1,000 results • Page
3 of 20
Recent Votes
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
> fastq-dump is deprecated Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
GenoMax
141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
BioinfGuru
★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO
by
GenoMax
141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
bp22
▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
Ram
43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★ 1.7k
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