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 : this year
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
6
votes
5
replies
5.2k
views
MA plots DESeq: strange MA plots
RNA-Seq
MAplot
DESeq
updated 12 months ago by
Ram
41k • written 8.4 years ago by
VHahaut
★ 1.1k
3
votes
4
replies
5.2k
views
How to visualize sequence quality control distribution
sequence
Fastq
R
updated 8 months ago by
Ram
41k • written 8.0 years ago by
faizlotfy
▴ 30
0
votes
0
replies
5.2k
views
Query deleterious score of SNP mutation for various prediction methods with UniProt ID and mutation position
SNP
updated 11 months ago by
Ram
41k • written 8.5 years ago by
ajingnk
▴ 130
0
votes
1
reply
5.1k
views
Plotting traits on phylogenetic tree in R - issue with aligning traits
traits
graphics
R
phylogenetic-tree
updated 10 months ago by
Ram
41k • written 8.5 years ago by
ch_at
▴ 10
3
votes
6
replies
5.1k
views
RNA-SEQ DEG -- No Control
RNA-Seq
updated 11 months ago by
Ram
41k • written 8.4 years ago by
cacampbell
▴ 50
6
votes
9
replies
5.1k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 8 months ago by
Ram
41k • written 8.6 years ago by
gaurav.singh
▴ 10
1
vote
5
replies
5.1k
views
How To Find The Total Number Of Reads Used By Trinity Assembler To Perform Assembly
trinity
RNA-seq
updated 9 months ago by
Ram
41k • written 9.9 years ago by
bambus0725
▴ 50
0
votes
4
replies
5.1k
views
Sequence alignment length
multiple-sequence-alignment
updated 6 months ago by
Ram
41k • written 6.8 years ago by
biobudhan
▴ 20
0
votes
3
replies
5.1k
views
Detecting outlier loci from pairwise Fst values
outlier
Fst
vcftools
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Earendil
▴ 50
0
votes
9
replies
5.0k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 3 months ago by
ATpoint
78k • written 4.6 years ago by
Joel Wallenius
▴ 180
1
vote
2
replies
5.0k
views
Transform VCF file for Rqtl input for genetic mapping
SNP
updated 12 months ago by
Ram
41k • written 8.4 years ago by
rajini28m
▴ 10
0
votes
1
reply
5.0k
views
Hapmap to vcf
vcf
hapmap
updated 4 months ago by
Ram
41k • written 5.2 years ago by
shinken123
▴ 150
4
votes
5
replies
5.0k
views
Comparing 2 pathway over-representation analyses
Fishers-exact
pathway-analysis
statistics
updated 11 months ago by
Ram
41k • written 8.6 years ago by
weeweedelivery123
▴ 40
3
votes
4
replies
5.0k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 4 months ago by
tirza.doniger
▴ 10 • written 8.3 years ago by
tiago211287
★ 1.4k
2
votes
4
replies
4.9k
views
What Is A Correct Way To Assess Batch Effect?
batch-effect
updated 9 months ago by
Ram
41k • written 10.5 years ago by
vanzetti
▴ 60
1
vote
2
replies
4.9k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
8 months ago by
andres.firrincieli
3.5k
0
votes
2
replies
4.9k
views
Arlequin Input format for Mismatch distribution
Arlequin
Mismatch-Distribution
Expansion
updated 11 months ago by
Ram
41k • written 8.4 years ago by
rimjhim.roy.ch
▴ 80
0
votes
4
replies
4.8k
views
Tajima'S D Test-Ngs Data
biology
genetics
updated 9 months ago by
Ram
41k • written 11.2 years ago by
jackuser1979
▴ 890
1
vote
3
replies
4.8k
views
Wgcna -Dilemma In Choosing Soft Threshold
r
updated 9 months ago by
Ram
41k • written 10.4 years ago by
pixie@bioinfo
★ 1.5k
7
votes
7
replies
4.7k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 6 months ago by
Ram
41k • written 4.9 years ago by
stu111538
▴ 80
6
votes
7
replies
4.7k
views
Creation Of A .Bed File From .Txt
plink
updated 8 months ago by
Ram
41k • written 9.8 years ago by
tom.d.brocklehurst
• 0
6
votes
6
replies
4.7k
views
MSD calculations vs time
MDsimulation
python
computational-biology
updated 12 months ago by
Ram
41k • written 8.4 years ago by
contact.lifesciences.inc
▴ 30
0
votes
1
reply
4.7k
views
Convert exonerate output to EVM gff3 format error
evidencemodeler
evm
gff3
exonerate
updated 10 months ago by
Ram
41k • written 8.6 years ago by
sun.nation
▴ 140
0
votes
6
replies
4.6k
views
Installing BioLinux 8 on Ubuntu 15.04
ubuntu
biolinux
updated 10 months ago by
Ram
41k • written 8.5 years ago by
waqas.ahmad5231
• 0
1
vote
2
replies
4.6k
views
Isfinder And Integrall Databases
metagenomics
INTEGRALL
ISFinder
BLAST
updated 8 months ago by
Ram
41k • written 9.8 years ago by
alielbehery
▴ 10
1
vote
4
replies
4.6k
views
TCGA data(RPKM) differential gene expression
rna-seq
R
TCGA
RPKM
IPA
5 months ago by
realnewbie
▴ 30
0
votes
5
replies
4.6k
views
Error during Trinity running with the recent version?
next-gen
Assembly
RNA-Seq
updated 9 months ago by
Ram
41k • written 8.6 years ago by
seta
★ 1.8k
1
vote
1
reply
4.6k
views
Downloading GenomeStudio on Mac
methylation-module
genome-studio
updated 8 months ago by
Ram
41k • written 5.1 years ago by
daniellemo
▴ 10
3
votes
6
replies
4.5k
views
Why Do I Get A Makeblastdb Error: File Does Not Match Input Format Type, Default Input Type Is Fasta
genomics
blast-plus
updated 9 months ago by
Ram
41k • written 10.0 years ago by
alok.helix
▴ 120
10
votes
14
replies
4.5k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 5 months ago by
Ram
41k • written 3.8 years ago by
gable_works
▴ 50
2
votes
7
replies
4.5k
views
SRA toolkit internet settings
sratoolkit
fastq-dump
sequencing
RNA-Seq
updated 5 months ago by
Ram
41k • written 7.3 years ago by
BCArg
▴ 70
3
votes
2
replies
4.5k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 4 months ago by
logbio
▴ 30 • written 4.0 years ago by
The
▴ 180
6
votes
7
replies
4.4k
views
8 follow
desktop bioinformatics platform specs
hardware
desktop
updated 11 months ago by
Ram
41k • written 8.4 years ago by
rob234king
▴ 610
0
votes
3
replies
4.4k
views
Annovar And Ubuntu 12.10 - Database Download
ubuntu
annovar
updated 8 months ago by
Ram
41k • written 10.7 years ago by
Achim
• 0
2
votes
12
replies
4.4k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 10 months ago by
Ram
41k • written 8.6 years ago by
cmogren
▴ 20
1
vote
2
replies
4.3k
views
i have installed seaborn with python2.7 but when I am importing seaborn through terminal itz showing following error:
seaborn
python2.7
updated 11 months ago by
Ram
41k • written 6.8 years ago by
naveen100787
• 0
3
votes
5
replies
4.3k
views
Sum of TPM values across all genes separates tumors from normals in some TCGA data sets -- what gives?
rsem
RNA-Seq
tcga
updated 11 months ago by
Ram
41k • written 8.5 years ago by
naxerova
▴ 20
1
vote
0
replies
4.3k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink
genomes
ancestrymap
updated 4 months ago by
Ram
41k • written 7.4 years ago by
Ghoul
▴ 10
0
votes
0
replies
4.3k
views
vcftools FORMAT ID error during filtering
vcf
vcftools
updated 9 months ago by
Ram
41k • written 8.6 years ago by
wickell.david
• 0
1
vote
3
replies
4.2k
views
Beagle Imputation Markers List
imputation
updated 9 months ago by
Ram
41k • written 10.5 years ago by
avik
▴ 60
1
vote
4
replies
4.2k
views
design primer for alternative splicing events
alternative-splicing
primer-design
RNA-Seq
updated 10 months ago by
Ram
41k • written 8.5 years ago by
pengchy
▴ 450
3
votes
2
replies
4.2k
views
Plotting "sequence alignments" in python (matplotlib)?
matplotlib
python
sequencing
gene
updated 12 months ago by
Ram
41k • written 8.4 years ago by
knpayne2
• 0
0
votes
9
replies
4.2k
views
Merge BAM files for a lane with multiplexed samples.
multiplexing
samtools
baserecalibrator
gatk
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Timothée Flutre
▴ 20
1
vote
1
reply
4.2k
views
deflated lambda value but inflated qq plot
r
gwas
qqplot
updated 11 months ago by
Ram
41k • written 8.5 years ago by
muralinmars
▴ 100
7
votes
4
replies
4.2k
views
IGV genome browser problems
igv
updated 12 months ago by
Ram
41k • written 8.4 years ago by
Marvin
▴ 210
0
votes
8
replies
4.2k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 3 months ago by
Ram
41k • written 5.0 years ago by
V
▴ 380
0
votes
4
replies
4.2k
views
problem in installing zlibbioc library
R
updated 10 months ago by
Ram
41k • written 8.5 years ago by
m_punisher6
• 0
3
votes
4
replies
4.1k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 3 months ago by
Ram
41k • written 5.1 years ago by
Teresa
▴ 20
1
vote
12
replies
4.1k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 10 months ago by
ATpoint
78k • written 6.2 years ago by
SMILE
▴ 170
2
votes
10
replies
4.1k
views
Error encountered while running stattest from ballgown package
bioconductor
RNA-Seq
ballgown
stattest
updated 7 months ago by
Ram
41k • written 6.6 years ago by
lakhujanivijay
5.8k
1,000 results • Page
2 of 20
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
Recent Locations •
All
Bologna,
7 minutes ago
Spain,
10 minutes ago
Hungary,
10 minutes ago
Italy,
13 minutes ago
United States,
15 minutes ago
Frankrike,
24 minutes ago
Tehran,
32 minutes ago
Recent Awards •
All
Popular Question
to
endre.sebestyen
▴ 10
Popular Question
to
beausoleilmo
▴ 560
Commentator
to
Brian Bushnell
19k
Popular Question
to
Gama313
▴ 120
Popular Question
to
nanodano
▴ 30
Popular Question
to
shome
▴ 10
Popular Question
to
Malachi Griffith
19k
Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
Traffic: 801 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