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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 1 day 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
3
replies
2.8k
views
Circos plot for ecoli genome
rna-seq
circos
updated 7 months ago by
Ram
43k • written 7.3 years ago by
raya.girish
▴ 30
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 5 hours ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
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
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
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
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
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 24 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 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
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
2
votes
3
replies
2.7k
views
Merge really large amount of Seurat objects
Seurat
9 months ago by
Andy
▴ 120
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
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
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 1 day ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
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 9 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 1 day 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
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
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
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
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
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
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
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 23 days ago by
Ram
43k • written 6.2 years ago by
Sharon
▴ 600
1,000 results • Page
3 of 20
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Recent Awards •
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Recent Replies
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
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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