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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
9.6k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
6.8 years ago by
midox
▴ 290
4
votes
45
replies
5.9k
views
SAM file wrong? help with validatesamfile
EXOME
Tutorial
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
3.9k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.4 years ago by
nazaninhoseinkhan
▴ 490
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
17
votes
37
replies
3.1k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.7 years ago by
Biostar
20 • written 3.8 years ago by
williamsbrian5064
▴ 470
3
votes
32
replies
2.3k
views
fastqc report for degradome reads
fastqc
adaptor
4.8 years ago by
Sam
▴ 150
8
votes
30
replies
3.3k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 2.9 years ago by
wm
▴ 550 • written 2.9 years ago by
Negin
▴ 20
14
votes
30
replies
2.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.7 years ago by
Malka
▴ 70
4
votes
30
replies
1.2k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
2.6 years ago by
stan.aanhane
▴ 30
4
votes
30
replies
1.3k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 2.5 years ago by
Ram
37k • written 2.5 years ago by
sami
▴ 30
7
votes
29
replies
1.4k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
4.2 years ago by
Chaimaa
▴ 260
11
votes
29
replies
7.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 15 months ago by
Ram
37k • written 8.6 years ago by
Parham
★ 1.6k
0
votes
29
replies
2.0k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 4.6 years ago by
Biostar
20 • written 4.8 years ago by
nour.hadjz
▴ 20
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.6 years ago by
Za
▴ 140
2
votes
28
replies
5.0k
views
Memory use in indexing
Assembly
software error
updated 4.5 years ago by
Ram
37k • written 4.7 years ago by
marongiu.luigi
▴ 670
9
votes
27
replies
5.7k
views
How do I use Glimmer 3.02?
sequencing
updated 4.0 years ago by
ojelizodun
• 0 • written 4.9 years ago by
nattzy94
▴ 50
4
votes
27
replies
3.4k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 2.1 years ago by
Biostar
20 • written 6.4 years ago by
JoeDoasi
▴ 10
3
votes
27
replies
4.4k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 4.5 years ago by
Shiqi Li
• 0 • written 4.6 years ago by
zeynep
▴ 10
1
vote
26
replies
4.2k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
4.0 years ago by
kushagraprasad24
• 0
8
votes
25
replies
1.8k
views
construction of a database
neo4j
noSQL
sql
bioinformatic
database
updated 20 months ago by
Michael Dondrup
52k • written 20 months ago by
Debut
▴ 20
24
votes
25
replies
5.3k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.5 years ago by
dpc
▴ 240
10
votes
25
replies
2.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.5 years ago by
Biostar
20 • written 4.6 years ago by
Za
▴ 140
13
votes
24
replies
3.2k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 5.9 years ago by
GenoMax
125k • written 5.9 years ago by
Gary
▴ 480
5
votes
24
replies
6.6k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
4.6 years ago by
DanielC
▴ 160
0
votes
24
replies
2.3k
views
converting spaces to tabs in gtf files
NCBI
21 months ago by
storm1907
▴ 30
11
votes
24
replies
3.8k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
3.7 years ago by
williamsbrian5064
▴ 470
1
vote
23
replies
944
views
FASTQ exctract ID's
fastq
3.1 years ago by
User000
▴ 620
10
votes
23
replies
1.7k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.2 years ago by
GenoMax
125k • written 5.2 years ago by
Farbod
★ 3.3k
1
vote
23
replies
928
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
2.4 years ago by
jmwhitha
• 0
6
votes
23
replies
2.0k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
4.6 years ago by
Charlie2
▴ 50
11
votes
22
replies
2.7k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
3.7 years ago by
RNAseqer
▴ 220
23
votes
22
replies
36k
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 8 weeks ago by
Nicole
• 0 • written 4.7 years ago by
gaelgarcia
▴ 250
5
votes
22
replies
2.4k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
4.6 years ago by
Biologist
▴ 260
1
vote
22
replies
2.3k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 4.2 years ago by
Kevin Blighe
84k • written 4.2 years ago by
carolgalah
• 0
0
votes
22
replies
2.4k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
4.8 years ago by
Muha0216
• 0
3
votes
22
replies
2.1k
views
samtools coverage usage
NGS
updated 19 months ago by
Lila M
★ 1.2k • written 19 months ago by
smrutimayipanda
▴ 20
5
votes
22
replies
6.3k
views
SVM for classified gene expression data
R
svm
microarray
updated 6 months ago by
Ram
37k • written 7.0 years ago by
Shaurya Jauhari
▴ 50
1
vote
22
replies
4.6k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
4.2 years ago by
olechnwin
▴ 60
13
votes
22
replies
8.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.4 years ago by
Biostar
20 • written 5.5 years ago by
lessismore
★ 1.3k
2
votes
22
replies
1.0k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
3 months ago by
Joel Wallenius
▴ 100
3
votes
22
replies
2.3k
views
Making RefSeq in Windows
refseq
6.5 years ago by
Alireza Ebadi Tabrizi
• 0
2
votes
21
replies
2.6k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 3.8 years ago by
Ram
37k • written 3.8 years ago by
pablo
▴ 230
1
vote
21
replies
1.7k
views
Center and scale RIN values for DESeq2?
deseq2
rin
2.4 years ago by
randalljellis
▴ 90
16
votes
21
replies
1.5k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.3 years ago by
Farbod
★ 3.3k
3
votes
21
replies
2.6k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 21 months ago by
Ram
37k • written 3.4 years ago by
mathavanbioinfo
▴ 70
0
votes
21
replies
1.4k
views
HTSeq-Count: no_feature too high?
htseq-count
3 months ago by
sea.joson
▴ 10
7
votes
21
replies
2.2k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
6.2 years ago by
jmsyl.hong
• 0
10
votes
21
replies
2.1k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.5 years ago by
Biostar
20 • written 3.5 years ago by
Miguel
▴ 10
6
votes
21
replies
1.9k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 4.3 years ago by
Biostar
20 • written 4.5 years ago by
afli
▴ 190
5
votes
20
replies
3.1k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 4 months ago by
Ram
37k • written 7.4 years ago by
Hans
▴ 130
1,000 results • Page
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Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Comment: Gene Set Enrichment Analysis, pathway, metabolism
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maxdlf12
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Teacher
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Pierre Lindenbaum
152k
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LDT
▴ 220
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Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
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152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
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but you already knew it. https://www.biostars.org/p/9551097/#9551098
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152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
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Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
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Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
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Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
Comment: Error: unable to open file or unable to determine types for file bed file
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Neel
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**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
Answer: Anti-miRNA oligonuclotide identification
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Asan Emirsale
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You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
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vaslanzadeh
▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
Answer: HISAT2 output direct to bam sorted
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ATpoint
68k
hisat2 --dta -x genome -1 ../fastq_zea_mays/SRR214880_1.fastq -2 ../fastq_zea_mays/SRR214880_2.fastq \ | samtools sort -o sorted.b…
Comment: Error: Please supply a reference FASTA/GBK/EMBL file with --reference
by
Neel
▴ 10
Yeah, its working now thank you so much for your reply.
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