Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
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
8.1 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
5.6k
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 2.0 years 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
2.4k
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
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
8
votes
30
replies
5.1k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 560 • 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
11
votes
29
replies
9.8k
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
0
votes
29
replies
3.0k
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
2
votes
28
replies
7.5k
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
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
3
votes
27
replies
5.6k
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
4
votes
27
replies
4.4k
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
9
votes
27
replies
7.6k
views
How do I use Glimmer 3.02?
sequencing
updated 5.3 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
10
votes
25
replies
3.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
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
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
4.6k
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
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
1
vote
23
replies
2.1k
views
FASTQ exctract ID's
fastq
4.4 years ago by
User000
▴ 690
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
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
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 16 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 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
5
votes
22
replies
7.5k
views
SVM for classified gene expression data
R
svm
microarray
updated 21 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 9 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
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
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
5.5 years ago by
olechnwin
▴ 60
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
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
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
▴ 90
0
votes
21
replies
1.1k
views
Expression analysis of LncRNA from RNA-seq data
expression
lncrna
11 weeks ago by
analyst
▴ 30
6
votes
21
replies
2.8k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.6 years ago by
Biostar
20 • written 5.7 years ago by
afli
▴ 190
7
votes
21
replies
3.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
0
votes
21
replies
2.7k
views
HTSeq-Count: no_feature too high?
htseq-count
18 months ago by
sea.joson
▴ 10
1
vote
21
replies
2.9k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.7 years ago by
randalljellis
▴ 90
1,000 results • Page
1 of 20
Recent Votes
How to normalize long-read RNA-seq data for comparison with short-reads
EdgeR analysis with CPM normalzed counts
Alternative splicing convention
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Recent Locations •
All
China,
1 minute ago
TÜRKİYE,
2 minutes ago
India,
2 minutes ago
Germany,
5 minutes ago
Germany,
7 minutes ago
France,
7 minutes ago
Australia,
7 minutes ago
Recent Awards •
All
Popular Question
to
sapuizait
▴ 10
Voter
to
analyst
▴ 30
Scholar
to
ATpoint
82k
Popular Question
to
zdiazmar
▴ 30
Popular Question
to
hkarakurt
▴ 180
Student
to
John Torcivia
▴ 70
Popular Question
to
bioinfo
▴ 150
Recent Replies
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt
by
Joe
21k
If you have the accession numbers can you not use something like `eutils`?
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
ATpoint
82k
For question 1: For question 1: Purpose of indexing a genome/transcriptome/book/anything: https://www.biostars.org/p/212594/ For question …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis
by
LauferVA
4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Traffic: 2745 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6