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
4 of 20
Sort: Views
Rank
Views
Votes
Replies
1
vote
7
replies
8.7k
views
How single sample GSEA works
ssgsea
RNA-seq
R
GSVA
updated 4.8 years ago by
Kevin Blighe
88k • written 4.8 years ago by
sugus
▴ 150
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.7 years ago by
Biostar
20 • written 7.5 years ago by
lu.ne
▴ 70
2
votes
9
replies
8.7k
views
How to highlight genes on a Manhattan plot
R
gene
SNP
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
kyoko777
• 0
5
votes
24
replies
8.7k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.9 years ago by
DanielC
▴ 170
18
votes
4
replies
8.7k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 14 months ago by
Ram
43k • written 10.8 years ago by
user
▴ 940
5
votes
4
replies
8.6k
views
GFF3 to GTF conversion - 9th column
gtf
NCBI
gff3
featureCounts
updated 21 months ago by
Ram
43k • written 8.3 years ago by
mrodrigues.fernanda
▴ 50
5
votes
17
replies
8.6k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.5 years ago by
C4
▴ 30
1
vote
7
replies
8.6k
views
merge two SeuratObjects to do the integration
RNA-Seq
3.8 years ago by
yueli7
▴ 250
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap
RNA-Seq
clustering
5.1 years ago by
CuriousGuy
▴ 90
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
hana
▴ 190
2
votes
7
replies
8.6k
views
Design matrix not of full rank.
RNA-Seq
edgeR
R
7.9 years ago by
firestar
★ 1.6k
0
votes
1
reply
8.5k
views
Purpose Of Y-Shaped Adapters In Illumina Sequencing?
illumina
adaptor
sequencing
rna-seq
11.0 years ago by
gaelgarcia05
▴ 280
1
vote
2
replies
8.5k
views
vcf compare between 2 vcf files using vcf tools
vcftools
updated 14 months ago by
Ram
43k • written 7.5 years ago by
bioguy24
▴ 230
6
votes
15
replies
8.5k
views
Strand specific protocol for bowtie2 alignment
bowtie2
rnaseq
alignment
RNA-Seq
updated 2.5 years ago by
Ram
43k • written 8.5 years ago by
nalandaatmi
▴ 100
2
votes
8
replies
8.5k
views
STAR mapping results
RNA-Seq
updated 4.5 years ago by
Biostar
20 • written 4.7 years ago by
mxlsherry1992
▴ 80
10
votes
6
replies
8.4k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.9 years ago by
alserg
▴ 930 • written 2.9 years ago by
gabrielbaldanzi
▴ 10
0
votes
7
replies
8.4k
views
Bio-DB-HTS installation and ensembl-vep
Bio-DB-HTS
ensembl
vep
updated 2.7 years ago by
al.bodrug
▴ 50 • written 5.2 years ago by
felipead66
▴ 120
1
vote
2
replies
8.4k
views
Awk- How to compare 2 files with common columns and then get the output file with columns from each file.
awk
7.6 years ago by
bright.g.january1732
• 0
2
votes
9
replies
8.4k
views
Map ensembl gene id form hg38 in hg19
sequencing
hg38
hg19
7.9 years ago by
Tanvir Ahamed
▴ 350
5
votes
20
replies
8.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.8 years ago by
varsha619
▴ 90
5
votes
3
replies
8.3k
views
Differential Gene Expression (EdgeR?) : What are the steps in computing this?
gene
rna
microarray
differential
expression
7.8 years ago by
O.rka
▴ 720
3
votes
4
replies
8.3k
views
RNA-Seq raw fastq files from TCGA
RNA-Seq
TCGA
fastq
7.4 years ago by
oriolebaltimore
▴ 190
2
votes
7
replies
8.3k
views
linux 'cat' command merge fasta files without headers
fasta
linux
updated 14 months ago by
Ram
43k • written 9.9 years ago by
esterbuiate
• 0
4
votes
5
replies
8.3k
views
Calculating FPKM from HTSeq counts table
RNA-Seq
R
HTSeq
fpkm
6.7 years ago by
ann081993
▴ 10
9
votes
11
replies
8.2k
views
8 follow
Extremely low mapping rates with bowtie2
alignment
next-gen
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
Sachin
▴ 10
0
votes
3
replies
8.2k
views
adding PCA ellipses on ggplot2
gene
RNA-Seq
ggplot2
pca
5.6 years ago by
demoraesdiogo2017
▴ 100
1
vote
2
replies
8.2k
views
How To Compute A Genetic Map For Snps
plink
snp
updated 10.7 years ago by
Biostar
20 • written 11.2 years ago by
Tim
▴ 10
0
votes
8
replies
8.2k
views
R providing row numbers instead row names with read.csv?
R
updated 3.9 years ago by
zx8754
11k • written 3.9 years ago by
blacktomato27
▴ 70
0
votes
1
reply
8.2k
views
How to solve error 'Error in split.default(X, group) : first argument must be a vector' in RepeatExplorer
software error
ngs
R
8.0 years ago by
namratapatel183
▴ 10
1
vote
4
replies
8.2k
views
Error when trying to install a package (non-zero exit status)
Packages
Bioconductor
updated 2.0 years ago by
jv
★ 1.8k • written 2.0 years ago by
BioC123
• 0
5
votes
1
reply
8.2k
views
*.rnk file preparation for GSEA analysis
RNA-Seq
GSEA
Enrichment analysis
R
webgestalt
4.7 years ago by
o.mikh90
▴ 30
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.8 years ago by
dpc
▴ 240
0
votes
2
replies
8.1k
views
How to solve error memory R package pedigree
pedigree
R
software error
memory
5.8 years ago by
Kian
▴ 50
2
votes
2
replies
8.1k
views
How to filter out special sequences from a fasta file based on sequence IDs txt
fasta
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Ginsea Chen
▴ 130
0
votes
4
replies
8.1k
views
Problem With Autodock 4.2.5
docking
updated 2.2 years ago by
Ram
43k • written 11.4 years ago by
Dollas Salleh
▴ 70
6
votes
9
replies
8.1k
views
Why we need 100X coverage to get a high-quality assembly?
genome
Assembly
PacBio
Coverage
7.5 years ago by
lamz138138
▴ 40
5
votes
1
reply
8.1k
views
Meaning Of Colors Used In Samtools Tview
samtools
11.4 years ago by
deepthithomaskannan
▴ 380
7
votes
12
replies
8.0k
views
How to identify ORFs in Python dictionaries
Python3
ORF
Open reading frame
python dictionaries
7.3 years ago by
ron
▴ 40
2
votes
1
reply
8.0k
views
ROH by PLINK
plink
ROH
updated 15 months ago by
Ram
43k • written 9.0 years ago by
afadda
▴ 20
2
votes
2
replies
8.0k
views
Is There A Website That Will Generate A Citation Or Collaboration Network For A Given Keyword(S) Or A Publication?
network
search
10.6 years ago by
Superbest
▴ 130
5
votes
14
replies
8.0k
views
Microrna Adapter Trimming
updated 10.4 years ago by
Fabio Marroni
★ 3.0k • written 10.5 years ago by
xiaojuhu13
▴ 150
1
vote
4
replies
8.0k
views
Polygenic Risk Score PLINK
plink
polygenic risk score
risk score
SNP scoring
updated 6.2 years ago by
rse
▴ 100 • written 7.5 years ago by
mzezza
▴ 10
1
vote
3
replies
8.0k
views
Calling differential peaks on ATAC-seq data
ATAC-seq
THOR
MACS2
Peak Calling
updated 2.7 years ago by
117010004
• 0 • written 7.2 years ago by
ldyer2006
▴ 50
1
vote
7
replies
8.0k
views
Unaligned Reads From Bowtie2
bowtie2
updated 2.4 years ago by
Ram
43k • written 10.5 years ago by
deepthithomaskannan
▴ 380
4
votes
2
replies
8.0k
views
PLINK Merge error: File write failure
plink
1000genomes
updated 20 months ago by
Ram
43k • written 8.6 years ago by
aritra90
▴ 70
0
votes
4
replies
8.0k
views
Potential issue setting breaks in R for heatmap? Getting different results in RStudio's Plots panel than Exporting PDF
R
heatmap
Rstudio
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
moldach
▴ 130
2
votes
4
replies
8.0k
views
Clustering data - data transformation (log2) highly improves clustering but why?
clustering
Elisa
data transformation
6.5 years ago by
JJ
▴ 680
2
votes
6
replies
7.9k
views
Heatmap using pheatmap issues
R
7.3 years ago by
1769mkc
★ 1.2k
1
vote
5
replies
7.9k
views
How To Retrieve Chromosome Lengths Using Bsgenome Package?
chromosome
length
10.6 years ago by
James Ashmore
▴ 100
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
43k • written 7.9 years ago by
cristina_sabiers
▴ 110
1,000 results • Page
4 of 20
Recent Votes
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
A: Filtering of VCF, INFO DP or FORMAT DP
What is the difference between GRCh37 and hs37? And hg19?
Answer: Duplicated sequence samtools
Recent Locations •
All
United States,
just now
Perth, Australia,
1 minute ago
United States,
8 minutes ago
Canada,
17 minutes ago
South Korea,
18 minutes ago
Russia,
20 minutes ago
United Kingdom,
21 minutes ago
Recent Awards •
All
Popular Question
to
RNAseqer
▴ 270
Scholar
to
kalavattam
▴ 190
Scholar
to
dthorbur
★ 2.0k
Commentator
to
Santosh Anand
5.7k
Popular Question
to
lagartija
▴ 160
Popular Question
to
bioinfo
▴ 150
Popular Question
to
Sara
▴ 30
Recent Replies
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation
by
Mathew
▴ 120
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database
by
Mathew
▴ 120
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error
by
Mathew
▴ 120
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database?
by
GenoMax
142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
GenoMax
142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Prawesh
• 0
I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Traffic: 1676 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