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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.2 years ago by
midox
▴ 290
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
18 months ago by
Leite
★ 1.2k
24
votes
25
replies
6.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.9 years ago by
dpc
▴ 240
23
votes
22
replies
40k
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 6 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
5.1k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 2.1 years ago by
Kevin Blighe
85k • written 5.3 years ago by
Joe
▴ 40
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 8 weeks ago by
Ram
39k • written 6.9 years ago by
Farbod
★ 3.4k
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.7 years ago by
fi1d18
★ 4.2k
20
votes
17
replies
5.2k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.8 years ago by
Anand Rao
▴ 560
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 10 months ago by
Ram
39k • written 7.4 years ago by
dam4l
▴ 190
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by
nazaninhoseinkhan
▴ 510
18
votes
19
replies
1.7k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 6 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
18
votes
7
replies
905
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
8 months ago by
Rafael Soler
★ 1.2k
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 3 months ago by
Ram
39k • written 9.8 years ago by
user
▴ 930
17
votes
8
replies
1.9k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.2 years ago by
nejc
▴ 50
17
votes
13
replies
5.6k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.1 years ago by
lghust2011
▴ 100
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 years ago by
Gian77
▴ 60
17
votes
37
replies
3.5k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.0 years ago by
Biostar
20 • written 4.2 years ago by
williamsbrian5064
▴ 470
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.9 years ago by
salamandra
▴ 540
16
votes
18
replies
4.1k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by
Mensur Dlakic
★ 23k • written 3.8 years ago by
tikshyadav19
• 0
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.7 years ago by
Farbod
★ 3.4k
16
votes
17
replies
2.8k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by
dimitrischat
▴ 180
16
votes
10
replies
4.9k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.0 years ago by
Alternative
▴ 270
16
votes
16
replies
2.5k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
5.2 years ago by
bioinfo456
▴ 150
16
votes
8
replies
1.7k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
chen
★ 2.4k
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 13 months ago by
Ram
39k • written 8.3 years ago by
Mo
▴ 920
15
votes
14
replies
2.4k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.4 years ago by
John
▴ 270
15
votes
14
replies
1.5k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.4 years ago by
Biostar
20 • written 5.6 years ago by
Mozart
▴ 330
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
Nadin.asal
• 0
14
votes
8
replies
4.6k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
9.7 years ago by
Dan D
7.4k
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
plink_9857
▴ 50
14
votes
16
replies
1.4k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.6 years ago by
lieven.sterck
14k • written 2.6 years ago by
utsafar
▴ 80
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 12 weeks ago by
Ram
39k • written 8.5 years ago by
f.muoghalu
• 0
14
votes
30
replies
2.6k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.1 years ago by
Malka
▴ 70
13
votes
7
replies
5.9k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
Raheleh
▴ 250
13
votes
13
replies
13k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
3.8 years ago by
Arindam Ghosh
▴ 500
13
votes
16
replies
5.7k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.4 years ago by
DNAngel
▴ 240
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
13
votes
13
replies
1.1k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.6 years ago by
DanielC
▴ 160
13
votes
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by
lauren.wahyudi
▴ 40
13
votes
11
replies
5.7k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.6 years ago by
jackgrayner
▴ 80
13
votes
13
replies
8.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.2 years ago by
Devon Ryan
103k • written 5.2 years ago by
amitgourav.ghosh12
▴ 70
13
votes
24
replies
3.5k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.2 years ago by
GenoMax
129k • written 6.2 years ago by
Gary
▴ 480
13
votes
16
replies
5.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.4 years ago by
Paul
★ 1.5k
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
lessismore
★ 1.3k
12
votes
12
replies
4.5k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 9.5 years ago by
Istvan Albert
98k • written 9.5 years ago by
biolab
★ 1.4k
12
votes
14
replies
4.6k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.3 years ago by
star
▴ 340
12
votes
17
replies
4.0k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
5.7 years ago by
anonymous1192976466
▴ 50
12
votes
10
replies
2.4k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.4 years ago by
John
13k
12
votes
28
replies
1.9k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.0 years ago by
Za
▴ 140
12
votes
4
replies
501
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
22 days ago by
Rafael Soler
★ 1.2k
1,000 results • Page
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Recent Votes
Comment: Italicise annotations with pheatmap
Visualizing Graph Alignment Format via minigraph
Gene prediction software
ClusterProfiler : What is GeneRatio and BgRatio?
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
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Recent Replies
Comment: Stratified sample assignment for analysis
by
ATpoint
72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph
by
colindaven
4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis
by
Vincent Laufer
★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴ 60
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
▴ 10
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
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