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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.5 years ago by
midox
▴ 290
4
votes
45
replies
6.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 6 months ago by
Ram
40k • written 7.3 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
4.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.1 years ago by
nazaninhoseinkhan
▴ 510
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 17 months ago by
Ram
40k • written 8.6 years ago by
Mo
▴ 920
17
votes
37
replies
4.0k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.3 years ago by
Biostar
20 • written 4.5 years ago by
williamsbrian5064
▴ 480
5
votes
35
replies
2.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 12 weeks ago by
Jordan M Eizenga
▴ 360 • written 3 months ago by
anivlete
• 0
3
votes
32
replies
2.9k
views
fastqc report for degradome reads
fastqc
adaptor
5.5 years ago by
Sam
▴ 150
4
votes
30
replies
1.9k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.2 years ago by
Ram
40k • written 3.2 years ago by
sami
▴ 30
14
votes
30
replies
2.9k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.4 years ago by
Malka
▴ 80
4
votes
30
replies
1.8k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.2 years ago by
stan.aanhane
▴ 30
8
votes
30
replies
4.3k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 3.5 years ago by
wm
▴ 550 • written 3.5 years ago by
Researcher
▴ 20
11
votes
29
replies
8.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 23 months ago by
Ram
40k • written 9.3 years ago by
Parham
★ 1.6k
7
votes
29
replies
2.0k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
4.8 years ago by
Chaimaa
▴ 260
0
votes
29
replies
2.4k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.3 years ago by
Biostar
20 • written 5.4 years ago by
nour.hadjz
▴ 20
2
votes
28
replies
6.3k
views
Memory use in indexing
Assembly
software error
updated 5.2 years ago by
Ram
40k • written 5.3 years ago by
marongiu.luigi
▴ 690
12
votes
28
replies
2.3k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.3 years ago by
Za
▴ 140
3
votes
27
replies
5.0k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 5.1 years ago by
Shiqi Li
• 0 • written 5.3 years ago by
zeynep
▴ 10
9
votes
27
replies
6.7k
views
How do I use Glimmer 3.02?
sequencing
updated 4.7 years ago by
ojelizodun
• 0 • written 5.5 years ago by
nattzy94
▴ 50
4
votes
27
replies
3.9k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 2.8 years ago by
Biostar
20 • written 7.1 years ago by
JoeDoasi
▴ 10
1
vote
26
replies
5.4k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
4.6 years ago by
kushagraprasad24
• 0
8
votes
25
replies
2.5k
views
construction of a database
sql
noSQL
neo4j
database
updated 6 months ago by
Ram
40k • written 2.4 years ago by
Debut
▴ 20
10
votes
25
replies
3.0k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
Za
▴ 140
24
votes
25
replies
7.0k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.2 years ago by
dpc
▴ 240
13
votes
24
replies
3.9k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.6 years ago by
GenoMax
135k • written 6.6 years ago by
Gary
▴ 480
5
votes
24
replies
7.8k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.3 years ago by
DanielC
▴ 160
11
votes
24
replies
4.7k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.4 years ago by
williamsbrian5064
▴ 480
0
votes
24
replies
3.0k
views
converting spaces to tabs in gtf files
NCBI
2.4 years ago by
storm1907
▴ 30
6
votes
23
replies
2.4k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
5.3 years ago by
Charlie2
▴ 50
10
votes
23
replies
2.0k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.9 years ago by
GenoMax
135k • written 5.9 years ago by
Farbod
★ 3.4k
1
vote
23
replies
1.5k
views
FASTQ exctract ID's
fastq
3.8 years ago by
User000
▴ 690
1
vote
23
replies
1.3k
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
3.1 years ago by
jmwhitha
• 0
11
votes
22
replies
3.4k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.4 years ago by
RNAseqer
▴ 250
23
votes
22
replies
43k
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 10 months ago by
Nicole
• 0 • written 5.4 years ago by
gaelgarcia
▴ 250
5
votes
22
replies
2.9k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.2 years ago by
Biologist
▴ 280
0
votes
22
replies
2.9k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
5.5 years ago by
Muha0216
• 0
1
vote
22
replies
2.9k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 4.8 years ago by
Kevin Blighe
86k • written 4.8 years ago by
carolgalah
• 0
4
votes
22
replies
3.7k
views
samtools coverage usage
NGS
updated 2.3 years ago by
Lila M
★ 1.2k • written 2.3 years ago by
smrutimayipanda
▴ 20
13
votes
22
replies
9.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 6.0 years ago by
Biostar
20 • written 6.2 years ago by
lessismore
★ 1.3k
3
votes
22
replies
2.7k
views
Making RefSeq in Windows
refseq
7.2 years ago by
Alireza Ebadi Tabrizi
• 0
1
vote
22
replies
5.5k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
4.9 years ago by
olechnwin
▴ 60
2
votes
22
replies
1.7k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
11 months ago by
Joel Wallenius
▴ 180
5
votes
22
replies
6.9k
views
SVM for classified gene expression data
R
svm
microarray
updated 14 months ago by
Ram
40k • written 7.7 years ago by
Shaurya Jauhari
▴ 50
2
votes
21
replies
3.4k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 4.5 years ago by
Ram
40k • written 4.5 years ago by
pablo
▴ 280
0
votes
21
replies
2.1k
views
HTSeq-Count: no_feature too high?
htseq-count
11 months ago by
sea.joson
▴ 10
6
votes
21
replies
2.4k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.0 years ago by
Biostar
20 • written 5.2 years ago by
afli
▴ 190
10
votes
21
replies
2.7k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.2 years ago by
Biostar
20 • written 4.2 years ago by
Miguel
▴ 10
1
vote
21
replies
2.3k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.1 years ago by
randalljellis
▴ 90
7
votes
21
replies
2.6k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
6.9 years ago by
jmsyl.hong
• 0
3
votes
21
replies
3.3k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 2.4 years ago by
Ram
40k • written 4.0 years ago by
mathavanbioinfo
▴ 70
16
votes
21
replies
1.8k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.0 years ago by
Farbod
★ 3.4k
1,000 results • Page
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Comment: How do you validate and verify your pipeline's software updates?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
Answer: Exporting DEGs obtained from DESeq2
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Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
• 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
• 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
• 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Total bases (number of reads * read length) should be calculated after removal of adapters, right?
Comment: Getting BLAST to give output whilst running
by
Ken
• 0
If I understand correctly, Blast can tell you how many results it has gotten but it can't tell you how many it is going to get, therefore i…
Comment: Understanding mother and father alleles in VCF file
by
Ram
40k
I don't understand your logic. You don't know what phasing is but are confident it is not required, and your proof is that relatives were d…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
It's from Nebula genomics. It must be possible to deduce parental alleles, since I converted the VCF file into a Myheritage VCF file and th…
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