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
2 of 20
Sort: Views
Rank
Views
Votes
Replies
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
7.0 years ago by
moxu
▴ 510
4
votes
9
replies
13k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
ste.lu
▴ 80
2
votes
13
replies
12k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 6.3 years ago by
basucsmcri
• 0 • written 7.2 years ago by
biostarsb
▴ 30
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 19 months ago by
Ram
43k • written 8.6 years ago by
Abdul Rafay Khan
★ 1.2k
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.1 years ago by
midox
▴ 290
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 7.7 years ago by
Biostar
20 • written 7.7 years ago by
rednalf
▴ 90
3
votes
8
replies
12k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
6.4 years ago by
a.rex
▴ 350
3
votes
2
replies
12k
views
ExAC PLI score calculation
DNA-Seq
7.2 years ago by
jonessara770
▴ 240
7
votes
9
replies
12k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 6.6 years ago by
Satyajeet Khare
★ 1.6k • written 6.6 years ago by
SMILE
▴ 170
2
votes
13
replies
12k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
8.3 years ago by
cacampbell
▴ 60
8
votes
5
replies
12k
views
samtools tview symbols
samtools
updated 17 months ago by
Ram
43k • written 8.8 years ago by
biolab
★ 1.4k
6
votes
7
replies
12k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
7.1 years ago by
abascalfederico
★ 1.2k
3
votes
4
replies
12k
views
basename: missing operand
snp
4.8 years ago by
evelyn
▴ 230
0
votes
3
replies
12k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
7.9 years ago by
BioICoder
▴ 40
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
1
vote
2
replies
12k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
7.8 years ago by
ilobelo
▴ 10
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 15 months ago by
Ram
43k • written 8.9 years ago by
che.bellaj
• 0
4
votes
14
replies
11k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
7.7 years ago by
kirannbishwa01
★ 1.6k
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 15 months ago by
Ram
43k • written 8.9 years ago by
ashishchahl
• 0
3
votes
4
replies
11k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
12.6 years ago by
Lisanne
• 0
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
10.9 years ago by
jeansimon32
▴ 170
2
votes
8
replies
11k
views
Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
igv
gff
reference
contigs
12.2 years ago by
Nickengland
▴ 130
2
votes
4
replies
11k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 2.3 years ago by
Ram
43k • written 12.2 years ago by
Reyhaneh
▴ 530
5
votes
9
replies
11k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 5.9 years ago by
Biostar
20 • written 6.1 years ago by
oars
▴ 200
6
votes
3
replies
11k
views
Sequence duplication levels-RNA Seq
RNA-Seq
updated 3.6 years ago by
joshua.theisen
▴ 30 • written 6.1 years ago by
makwana.kd
▴ 50
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 7 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
2
votes
0
replies
11k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics
ordiellipse
vegan
R
phyloseq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
c.v.oflynn
▴ 100
4
votes
11
replies
11k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
20 months ago by
prasundutta87
▴ 660
7
votes
8
replies
11k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
6.5 years ago by
blur
▴ 280
3
votes
6
replies
11k
views
6 follow
How to calculate genetic correlation with R
R
updated 23 months ago by
ibomsolomon
• 0 • written 10.0 years ago by
Tohamy
▴ 80
2
votes
2
replies
10k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
5.0 years ago by
John
▴ 270
2
votes
8
replies
10k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 21 months ago by
zx8754
11k • written 3.2 years ago by
aradhana
• 0
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 20 months ago by
Ram
43k • written 8.6 years ago by
stevenlang123
▴ 210
3
votes
2
replies
10k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
7.9 years ago by
SOHAIL
▴ 400
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
10k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 15 months ago by
Ram
43k • written 8.9 years ago by
neokao
• 0
5
votes
2
replies
10k
views
Turning Seq objects into strings
sequence
5.1 years ago by
schlogl
▴ 160
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
10.8 years ago by
TitoPullo
▴ 180
1
vote
2
replies
10k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 6.3 years ago by
Biostar
20 • written 6.3 years ago by
fhassanz
▴ 20
2
votes
8
replies
10k
views
Size of typical genomic data
genomic
updated 13 months ago by
Ram
43k • written 5.9 years ago by
Nicolas Rosewick
10k
7
votes
9
replies
10k
views
Samtools Index Segmentation Fault
samtools
index
10.1 years ago by
Noushin N
▴ 600
1
vote
7
replies
10k
views
How to find up-regulated and down-regulated genes after GEO2R analysis?
GEO
genes
up-regulated
down-regulated
GEO2R
6.1 years ago by
DanielC
▴ 170
2
votes
4
replies
10k
views
num_threads with blastn in blast 2.6.0+
blast
5.3 years ago by
navela78
▴ 70
0
votes
1
reply
10k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA
statistics
metagenomics
updated 3.3 years ago by
dqq102829
• 0 • written 4.3 years ago by
zhangdengwei
▴ 210
3
votes
3
replies
10k
views
bcftools mpileup output format
bcftools
mpileup
5.7 years ago by
tarek.mohamed
▴ 360
1
vote
5
replies
10k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 4.2 years ago by
Karma
▴ 310 • written 10.4 years ago by
newDNASeqer
▴ 760
0
votes
0
replies
10k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
10.3 years ago by
jfertaj
▴ 110
3
votes
4
replies
10k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 6.6 years ago by
Ram
43k • written 6.6 years ago by
KVC_bioinfo
▴ 590
1
vote
1
reply
10k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
JackBel
• 0
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 2.3 years ago by
Ram
43k • written 9.8 years ago by
BDK_compbio
▴ 140
1,000 results • Page
2 of 20
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
Recent Locations •
All
California, USA,
1 minute ago
United States,
5 minutes ago
Poland,
10 minutes ago
Brazil,
12 minutes ago
Russia,
15 minutes ago
United States,
16 minutes ago
United States,
18 minutes ago
Recent Awards •
All
Popular Question
to
Simone
▴ 10
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
daffodil
▴ 10
Popular Question
to
Russ
▴ 500
Popular Question
to
camillab.
▴ 160
Popular Question
to
pramach1
▴ 40
Popular Question
to
Adyasha
• 0
Recent Replies
Answer: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Traffic: 2028 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