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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.0 years ago by
midox
▴ 290
4
votes
45
replies
7.7k
views
SAM file wrong? help with validatesamfile
EXOME
updated 12 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
5.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
17
votes
37
replies
4.7k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.9 years ago by
Biostar
20 • written 5.0 years ago by
williamsbrian5064
▴ 510
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
3
votes
32
replies
3.4k
views
fastqc report for degradome reads
fastqc
adaptor
6.0 years ago by
Sam
▴ 150
4
votes
30
replies
2.3k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.8 years ago by
stan.aanhane
▴ 30
4
votes
30
replies
2.4k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.7 years ago by
Ram
43k • written 3.7 years ago by
sami
▴ 40
8
votes
30
replies
5.1k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 550 • written 4.1 years ago by
Researcher
▴ 20
14
votes
30
replies
3.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
5.0 years ago by
Malka
▴ 80
0
votes
29
replies
2.9k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
nour.hadjz
▴ 20
7
votes
29
replies
2.4k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
5.4 years ago by
Chaimaa
▴ 260
11
votes
29
replies
9.7k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
12
votes
28
replies
2.7k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
2
votes
28
replies
7.4k
views
Memory use in indexing
Assembly
software error
updated 5.7 years ago by
Ram
43k • written 5.9 years ago by
marongiu.luigi
▴ 710
4
votes
27
replies
4.3k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 3.4 years ago by
Biostar
20 • written 7.7 years ago by
JoeDoasi
▴ 10
3
votes
27
replies
5.5k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 5.7 years ago by
Shiqi Li
• 0 • written 5.9 years ago by
zeynep
▴ 10
9
votes
27
replies
7.5k
views
How do I use Glimmer 3.02?
sequencing
updated 5.2 years ago by
ojelizodun
• 0 • written 6.1 years ago by
nattzy94
▴ 50
3
votes
26
replies
1.9k
views
6 follow
STAR Genome index Error
STAR
updated 6 months ago by
Ram
43k • written 6 months ago by
Prasanna
• 0
1
vote
26
replies
6.2k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
5.2 years ago by
kushagraprasad24
• 0
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.7 years ago by
dpc
▴ 240
8
votes
25
replies
3.0k
views
construction of a database
sql
noSQL
neo4j
database
updated 13 months ago by
Ram
43k • written 2.9 years ago by
Debut
▴ 20
10
votes
25
replies
3.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
5
votes
24
replies
8.7k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.9 years ago by
DanielC
▴ 170
0
votes
24
replies
3.5k
views
converting spaces to tabs in gtf files
NCBI
3.0 years ago by
storm1907
▴ 30
11
votes
24
replies
5.4k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 510
13
votes
24
replies
4.5k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.1 years ago by
GenoMax
141k • written 7.1 years ago by
Gary
▴ 480
1
vote
23
replies
2.0k
views
FASTQ exctract ID's
fastq
4.3 years ago by
User000
▴ 690
1
vote
23
replies
1.7k
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
3.6 years ago by
jmwhitha
• 0
10
votes
23
replies
2.4k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 6.4 years ago by
GenoMax
141k • written 6.4 years ago by
Farbod
★ 3.4k
6
votes
23
replies
2.9k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
5.8 years ago by
Charlie2
▴ 50
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 9 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
23
votes
22
replies
49k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 16 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
1
vote
22
replies
3.5k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 5.4 years ago by
Kevin Blighe
87k • written 5.4 years ago by
carolgalah
• 0
3
votes
22
replies
3.1k
views
Making RefSeq in Windows
refseq
7.7 years ago by
Alireza Ebadi Tabrizi
• 0
2
votes
22
replies
2.3k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
18 months ago by
Joel Wallenius
▴ 210
0
votes
22
replies
3.3k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
6.0 years ago by
Muha0216
• 0
5
votes
22
replies
7.5k
views
SVM for classified gene expression data
R
svm
microarray
updated 20 months ago by
Ram
43k • written 8.3 years ago by
Shaurya Jauhari
▴ 50
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 1 day ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
4
votes
22
replies
5.5k
views
samtools coverage usage
NGS
updated 2.8 years ago by
Lila M
★ 1.2k • written 2.8 years ago by
smrutimayipanda
▴ 20
1
vote
22
replies
6.2k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
5.4 years ago by
olechnwin
▴ 60
5
votes
22
replies
3.3k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.8 years ago by
Biologist
▴ 290
2
votes
21
replies
4.1k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 5.1 years ago by
Ram
43k • written 5.1 years ago by
pablo
▴ 300
0
votes
21
replies
2.7k
views
HTSeq-Count: no_feature too high?
htseq-count
17 months ago by
sea.joson
▴ 10
3
votes
21
replies
3.8k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 3.0 years ago by
Ram
43k • written 4.6 years ago by
mathavanbioinfo
▴ 80
7
votes
21
replies
3.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.4 years ago by
jmsyl.hong
• 0
0
votes
21
replies
1.0k
views
Expression analysis of LncRNA from RNA-seq data
expression
lncrna
9 weeks ago by
analyst
▴ 20
1
vote
21
replies
2.9k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.6 years ago by
randalljellis
▴ 90
12
votes
21
replies
3.2k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
Miguel
▴ 30
1,000 results • Page
1 of 20
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
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
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.
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