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: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
7
views
Finding a known duplication mutation in a VCF file
vcf
duplication
mutations
just now by
langzvi
• 0
0
votes
0
replies
6
views
Finding common pattern among heterogenous group of cancer
rnaseq
sequencing
19 minutes ago by
Hyper_Odin
▴ 240
0
votes
0
replies
18
views
How to compare two sequence logo?
bioinformatics
52 minutes ago by
Andrew Liu
▴ 10
0
votes
0
replies
9
views
Snakemake cluster execution error
cluster
snakemake
conda
1 hour ago by
blackadder
• 0
0
votes
1
reply
18
views
doubts about SNAP, bioinformatic tools for gene prediction
gene
prediction
updated 51 minutes ago by
lieven.sterck
14k • written 1 hour ago by
JUAN LUIS
• 0
0
votes
2
replies
57
views
How to find average read length and number of reads in a bam file using samtools in linux?
bam
sequencing
read
samtools
1 hour ago by
MobiusT
• 0
1
vote
2
replies
51
views
Tool similar to CollectGcBiasMetrics
metrics
picards
bioinformatics
gcbias
tool
1 hour ago by
tea.vuki
▴ 10
0
votes
0
replies
40
views
Gene ontology enrichment vs. REACTOME pathway analysis
GO
REACTOME
5 hours ago by
Gene_MMP8
▴ 210
0
votes
0
replies
35
views
mRNA contamination in miRNA prep
RIN
miRNA
5 hours ago by
Abhishek
• 0
0
votes
0
replies
33
views
extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq
non-coding
small
RNA-seq
miRNA
analysis
RNA
clustering
6 hours ago by
Rey
• 0
0
votes
0
replies
39
views
TCGA CIMP status
Bioinformatics
TCGA
COAD
6 hours ago by
ilomilo
• 0
0
votes
0
replies
67
views
PCA and logistic regression in GWAS
logistic
GWAS
PCA
regression
13 hours ago by
gosssheen
• 0
0
votes
2
replies
95
views
PCA plot for miRNA
miRNA
PCA
4 hours ago by
struggler
• 0
0
votes
6
replies
163
views
Ribosomal Depletion
rRNA
STAR
sequencing
contamination
RNA
updated 14 hours ago by
andres.firrincieli
★ 2.5k • written 16 hours ago by
kcarery
• 0
0
votes
2
replies
113
views
Error with TCGA package - TCGAbiolinks
TCGA
r
cancer
just now by
JACKY
▴ 10
0
votes
0
replies
58
views
Question about rMATS output files
rMATS
novel
20 hours ago by
Lillian
• 0
0
votes
1
reply
83
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA
r
cBioPortal
cancer
updated 41 minutes ago by
Friederike
8.4k • written 1 day ago by
JACKY
▴ 10
1
vote
0
replies
129
views
gene strand determined by flag in read1 and read2 should be intepreted differently?
bam
flag
samtools
RNA-seq
1 day ago by
tomas4482
▴ 140
0
votes
0
replies
123
views
Estimating gene family size changes for a large tree?
Phylogenetics
CAFE5
1 day ago by
Rijan
▴ 30
0
votes
1
reply
122
views
converting a DocumentTermMatrix to factor
DocumentTermMatrix
convert
factor
offtopic
updated 1 day ago by
cpad0112
20k • written 2 days ago by
hasani.iut6
▴ 70
0
votes
0
replies
102
views
Rooting a tree based on taxonomy of species
phylogeny
2 days ago by
lagartija
▴ 150
1
vote
0
replies
137
views
VQSR bias against rare variants
GATK
variant
VQSR
callling
2 days ago by
drabiza1
▴ 10
0
votes
0
replies
138
views
How do blastp step in MCScanX
MCScanX
2 days ago by
carlosgonzalezcruz327
▴ 10
0
votes
2
replies
235
views
Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly)
human
assembly
transcriptome
2 days ago by
Katherine
• 0
0
votes
3
replies
182
views
Incomplete alignment EMBOSS needleall
Alignment
updated 2 days ago by
lieven.sterck
14k • written 2 days ago by
bioinformatics.queries
▴ 50
0
votes
0
replies
113
views
TCGA data downloaded from GDC
TCGA
2 days ago by
Mamta
▴ 500
4
votes
4
replies
223
views
what is better to use in single cell
genomics
offtopic
updated 2 days ago by
Friederike
8.4k • written 2 days ago by
Bioinfo
• 0
0
votes
4
replies
241
views
Difference in number of DEGs from Deseq2 and limma-voom
RNAseq
Deseq2
limma
2 days ago by
dzisis1986
▴ 40
0
votes
2
replies
162
views
Gene expression assay Yeast sample prep
in
cells
Live
study
2 days ago by
dshdixit
▴ 10
1
vote
1
reply
191
views
ggscatter, gene expression, correlation
RNA-Seq
plot
scatter
updated 2 days ago by
Trivas
▴ 370 • written 3 days ago by
Rob
▴ 120
1
vote
0
replies
111
views
Interpretation of '1|2' in GT field and '0|1' in PGT field
GVCF
calling
GATK
SNP
VCF
2 days ago by
Choi
▴ 10
0
votes
0
replies
112
views
Cell Type and Gene Specific Survival Analysis in scRNA-seq
TCGA
scRNA-seq
3 days ago by
Ergün
▴ 20
0
votes
4
replies
214
views
how to get a sequence from read fragments with ref sequence?
reads
fragments
reference
assembly
sequence
4 hours ago by
Aaron
• 0
0
votes
1
reply
146
views
metagenome binning using MaxBin2 for each dataset
Metagenome
Binning
MaxBin
updated 2 days ago by
andres.firrincieli
★ 2.5k • written 3 days ago by
serene.s
• 0
1
vote
4
replies
266
views
bcftools index error: [E::bgzf_read_block] Invalid BGZF header at offset 12889964510
bcftools
updated 2 days ago by
cmdcolin
★ 2.2k • written 3 days ago by
biostars
▴ 10
0
votes
1
reply
165
views
Get cleaved SARS-CoV-2 protein sequences (all major variants)?
motif
variant
Python
SARS-CoV-2
cleavage
updated 3 days ago by
GenoMax
117k • written 3 days ago by
ngarber
• 0
0
votes
0
replies
150
views
How do I run pal2nal.pl in batch mode ?
gene
genome
protein
3 days ago by
Ramana
• 0
0
votes
0
replies
140
views
Converting GP field in a VCF to GT
VCF
GT
GP
3 days ago by
Garan
▴ 680
0
votes
0
replies
115
views
ReLERNN error
Genomics
ReLERNN
Problem
Error
3 days ago by
Javier
• 0
0
votes
0
replies
115
views
Hi-C data analysis (Loop and domain calling)
calling
and
Hi-C
HOMER
domain
Loop
3 days ago by
arsala521
▴ 10
0
votes
8
replies
312
views
How to ensure all fonts are written in Arial?
EnhancedVolcano
updated 2 days ago by
GenoMax
117k • written 3 days ago by
junli1988
• 0
2
votes
4
replies
208
views
Pymol superimposition by python script
python
superimposition
pymol
3 days ago by
iamsmor
• 0
0
votes
3
replies
151
views
splitting a bam file by XA tag into multiple lines
bam
tag
XA
file
BWA
3 days ago by
eric.londin
▴ 50
0
votes
2
replies
102
views
Bedtools Getfasta in snakemake
Bedtools
Snakemake
Wildcards
3 days ago by
Fadwa
▴ 10
0
votes
2
replies
164
views
gffcompare
RNA-seq
1 day ago by
linjc.xmu
▴ 30
0
votes
1
reply
99
views
Wildcards Snakemake using bedtools
Bedtools
Snakemake
Wildcards
updated 3 days ago by
Shred
▴ 640 • written 3 days ago by
Fadwa
▴ 10
0
votes
2
replies
101
views
Distinguish technical duplicates from biological duplicates
Duplicates
WGS
PCR
3 days ago by
BioStar22
• 0
0
votes
2
replies
106
views
SNPolisher_v1.5.0
AffyPipe
APT
Affymetrix
SNPolisher
3 days ago by
BiostarNewbie
• 0
0
votes
0
replies
75
views
How to (or not to) interpret the annotation abundance result from metagenome
gene
abundance
GO
annotation
metagenome
3 days ago by
young_bioinformatician
▴ 170
0
votes
1
reply
83
views
bwa mem for multiple paired read samples FastQfiles
fastq
reads
mem
bwa
paired
updated 3 days ago by
Pierre Lindenbaum
146k • written 3 days ago by
salman_96
▴ 50
1,000 results • Page
1 of 20
Recent Votes
Comment: Getting the best of RNA-Seq
Comment: Getting the best of RNA-Seq
Answer: bash script for merging R1 and R2 reads
Answer: Question regarding normalization in Seurat
Gzip output of fasterq-dump
DESeq2 converting numeric to factor for unknown reason - SOLVED
DESeq2 converting numeric to factor for unknown reason - SOLVED
Recent Locations •
All
Qatar,
just now
VIB, Ghent, Belgium,
just now
Australia,
just now
Lebanon,
just now
Egypt,
2 minutes ago
Berlin,
3 minutes ago
Italy,
3 minutes ago
Recent Awards •
All
Teacher
to
GenoMax
117k
Popular Question
to
Apex92
▴ 200
Scholar
to
AsoInfo
▴ 300
Popular Question
to
Gene_MMP8
▴ 210
Popular Question
to
Abhishek
• 0
Scholar
to
JACKY
▴ 10
Scholar
to
Marco Pannone
▴ 290
Recent Replies
Comment: Error with TCGA package - TCGAbiolinks
by
JACKY
▴ 10
Thank you @kevinblighe
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★ 4.8k
> The DESeq2 vignette offers a pretty comprehensive run-down of the entire process, starting with read quantification import and listing th…
Comment: Survival analysis based on a set of genes for TCGA data
by
yussufhajjaj93
• 0
Hi Hamid, thank you so much for the tutorial! But I wanted to ask if there a simple way to classify the data into quartiles or tertiles usi…
Comment: Getting the best of RNA-Seq
by
GenoMax
117k
> one being that not DE genes are expressed, and the other giving > rational but inaccurate DE expression Sounds like your experiment is n…
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★ 4.8k
> What do you mean by "rational, but inaccurate DE expression"? How do you gauge both rationality as well as accuracy of your results? B…
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★ 4.8k
This is the actual problem. If you are using as reference for the mapping a fasta file containing isoforms, your analysis should be address…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
Friederike
8.4k
If these are unsorted files, why would you need the last read? Couldn't you pick a random read or the first one?
Comment: Getting the best of RNA-Seq
by
Friederike
8.4k
>To mention, I started to use Kallisto and DESeq2 to see that after importing the data with the tximport package using the txOut = FALSE or…
Comment: Searching for RNA-seq melanoma samples in TCGA or cBioPortal
by
Friederike
8.4k
Can you specify a bit more what the end goal is? I.e. what type of data (processed, raw, ...) would you like to download and what would you…
Comment: Align short sequence against ONT reads
by
Friederike
8.4k
Are the long reads very different from each other (e.g. covering different regions of the genome) or do they all represent the same (more o…
Answer: Clustered, annotated dotplot to scRNA-Seq data
by
Friederike
8.4k
The [`dittoSeq`](https://github.com/dtm2451/DittoSeq) package also offers a [`dotPlot` function](http://bioconductor.org/packages/release/b…
Comment: doubts about SNAP, bioinformatic tools for gene prediction
by
lieven.sterck
14k
Hello https://www.biostars.org/u/110969/, Welcome to the forum! Please use the formatting bar (especially the `code` option) to present y…
Comment: How to find average read length and number of reads in a bam file using samtools
by
MobiusT
• 0
The size is 24661059 and I waited aroun 10 mins
Comment: Getting the best of RNA-Seq
by
ATpoint
62k
It is unclear to me what the question is. Do you want gene-level or transcript-level analysis? From what I know gene level analysis does no…
Answer: Computationally generated transcriptional regulation network
by
Matthias Zepper
▴ 910
Unfortunately, I have no experience whatsoever with yeast or GRN, but I recall [this article by de Boer et al.][1] that might be helpful. I…
Traffic: 1773 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