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: Votes
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
27
votes
17
replies
19k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
21 months ago by
Leite
★ 1.2k
24
votes
25
replies
6.9k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.2 years ago by
dpc
▴ 240
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 9 months ago by
Nicole
• 0 • written 5.4 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
5.3k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 2.4 years ago by
Kevin Blighe
86k • written 5.6 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 5 months ago by
Ram
40k • written 7.2 years ago by
Farbod
★ 3.4k
22
votes
19
replies
2.7k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.0 years ago by
fi1d18
★ 4.2k
20
votes
17
replies
5.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.1 years ago by
Anand Rao
▴ 560
20
votes
15
replies
27k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 13 months ago by
Ram
40k • written 7.7 years ago by
dam4l
▴ 190
20
votes
17
replies
2.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 weeks ago by
1769mkc
★ 1.1k • written 2.6 years ago by
pomodoro_sinensis
▴ 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
18
votes
4
replies
8.3k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 6 months ago by
Ram
40k • written 10.1 years ago by
user
▴ 940
18
votes
19
replies
1.9k
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 9 months ago by
Ram
40k • written 4.7 years ago by
rbkh09
• 0
18
votes
7
replies
1.1k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
12 months ago by
Rafael Soler
★ 1.2k
17
votes
8
replies
2.1k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.5 years ago by
nejc
▴ 50
17
votes
13
replies
5.9k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.4 years ago by
lghust2011
▴ 110
17
votes
19
replies
2.4k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.1 years ago by
Gian77
▴ 60
17
votes
37
replies
3.9k
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
16
votes
18
replies
4.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.1 years ago by
Mensur Dlakic
★ 24k • written 4.1 years ago by
tikshyadav19
• 0
16
votes
16
replies
2.7k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
5.5 years ago by
bioinfo456
▴ 150
16
votes
10
replies
5.1k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.3 years ago by
Alternative
▴ 270
16
votes
14
replies
15k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.2 years ago by
salamandra
▴ 550
16
votes
17
replies
2.9k
views
6 follow
RNA seq pipeline
RNA-Seq
5.9 years ago by
dimitrischat
▴ 200
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
16
votes
21
replies
1.7k
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
15
votes
14
replies
2.7k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.7 years ago by
John
▴ 270
15
votes
19
replies
1.6k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.4 years ago by
Ram
40k • written 5.4 years ago by
Nadin.asal
• 0
15
votes
14
replies
1.6k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.7 years ago by
Biostar
20 • written 5.9 years ago by
Mozart
▴ 330
14
votes
8
replies
4.7k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
10.0 years ago by
Dan D
7.4k
14
votes
18
replies
4.4k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
plink_9857
▴ 50
14
votes
16
replies
1.6k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.9 years ago by
lieven.sterck
14k • written 2.9 years ago by
utsafar
▴ 80
14
votes
5
replies
2.9k
views
bioinformatics basic training
genome
updated 6 months ago by
Ram
40k • written 8.8 years ago by
f.muoghalu
• 0
14
votes
30
replies
2.8k
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
▴ 70
13
votes
7
replies
6.1k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.8 years ago by
Biostar
20 • written 6.8 years ago by
Raheleh
▴ 260
13
votes
13
replies
8.3k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.5 years ago by
Devon Ryan
103k • written 5.5 years ago by
amitgourav.ghosh12
▴ 70
13
votes
16
replies
5.4k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.7 years ago by
Paul
★ 1.5k
13
votes
13
replies
15k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.1 years ago by
Arindam Ghosh
▴ 510
13
votes
11
replies
6.2k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.9 years ago by
jackgrayner
▴ 80
13
votes
13
replies
1.2k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.9 years ago by
DanielC
▴ 160
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
13
votes
24
replies
3.8k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.5 years ago by
GenoMax
134k • written 6.5 years ago by
Gary
▴ 480
13
votes
19
replies
4.8k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.8 years ago by
bioplanet
▴ 60
13
votes
6
replies
11k
views
6 follow
MAF vs VAF
sequencing
5.5 years ago by
lauren.wahyudi
▴ 40
13
votes
16
replies
6.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.7 years ago by
DNAngel
▴ 240
12
votes
12
replies
4.7k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 9.8 years ago by
Istvan Albert
98k • written 9.8 years ago by
biolab
★ 1.4k
12
votes
28
replies
2.2k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.3 years ago by
Za
▴ 140
12
votes
10
replies
2.6k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.7 years ago by
John
13k
12
votes
14
replies
5.1k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.6 years ago by
star
▴ 350
12
votes
8
replies
2.9k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.7 years ago by
statfa
▴ 740
12
votes
13
replies
2.4k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 9 months ago by
Ram
40k • written 8.2 years ago by
sarathkurichiyil
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: Identifying common DEGs among multiple datasets
Answer: Identifying common DEGs among multiple datasets
A: what do the headers of the rMATS output files mean?
A: what do the headers of the rMATS output files mean?
Answer: DESeq2 analysis using two featureCounts generated from different studies
Answer: DESeq2 analysis using two featureCounts generated from different studies
Answer: Assistance with Fungal Genome Annotation Using Maker and BLAST
Recent Locations •
All
Germany,
3 minutes ago
Australia,
3 minutes ago
United Arab Emirates,
3 minutes ago
New Delhi,
9 minutes ago
Norway,
9 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
10 minutes ago
Singapore,
17 minutes ago
Recent Awards •
All
Scholar
to
Pierre Lindenbaum
157k
Teacher
to
Michael
53k
Teacher
to
seidel
11k
Popular Question
to
jabaron.phd
• 0
Commentator
to
ATpoint
76k
Scholar
to
GenoMax
134k
Popular Question
to
Morgan S.
▴ 80
Recent Replies
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
Yes, definitely lots of noise and few peaks for such an experiment. Which celltype is that, and which lab protocol did you use?
Comment: DESeq2 analysis using two featureCounts generated from different studies
by
abedkurdi10
▴ 190
What do you mean by gene lists?
Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
• 0
Thank you so much for your responses. @genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★ 24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
camillab.
▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Traffic: 2162 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