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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 10 months ago by
Ram
43k • written 6.6 years ago by
steve
★ 3.5k
28
votes
11
replies
19k
views
9 follow
Salary For A Bioinformatics Programmer In Europe?
career
updated 10 months ago by
Ram
43k • written 12.6 years ago by
Jeroen Van Goey
2.3k
14
votes
3
replies
19k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 7 months ago by
William
▴ 30 • written 7.0 years ago by
kirannbishwa01
★ 1.6k
24
votes
15
replies
19k
views
7 follow
how can I remove duplicated variants from vcf file?
SNP
vcf
updated 7 months ago by
Ram
43k • written 6.7 years ago by
kk.mahsa
▴ 140
14
votes
17
replies
19k
views
6 follow
HISAT2 command help
RNA-Seq
alignment
updated 11 weeks ago by
DareDevil
★ 4.3k • written 8.2 years ago by
dina.hesham139
▴ 170
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 9 months ago by
Ram
43k • written 8.0 years ago by
John
13k
2
votes
5
replies
19k
views
FastQC command line usage
command-line
FastQC
linux
CentOS
updated 8 months ago by
Kermit
▴ 90 • written 2.1 years ago by
biology_inform
▴ 50
8
votes
6
replies
19k
views
Converting gtf format to bed format
bed
updated 3 months ago by
Apex92
▴ 280 • written 9.4 years ago by
thjnant
▴ 160
26
votes
9
replies
18k
views
8 follow
Favorite Splice Site Prediction/Evaluation Tools
splicing
prediction
updated 9 months ago by
abhilashdasari.10
▴ 30 • written 11.3 years ago by
Alex Paciorkowski
3.5k
176
votes
46
replies
18k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
4 months ago by
Istvan Albert
100k
0
votes
8
replies
18k
views
How to get subset of a Seurat object based on metadata?
scRNA-seq
Seurat
updated 12 months ago by
fracarb8
★ 1.5k • written 12 months ago by
sunyeping
▴ 110
38
votes
26
replies
18k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.1 years ago by
biostart
▴ 370
83
votes
34
replies
18k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
28
votes
7
replies
18k
views
6 follow
VCF merge or concatenate?
snp
VCF
VCFTools
written 4.7 years ago by
rokragna295
▴ 60
15
votes
9
replies
18k
views
8 follow
How to count fasta sequences efficiently using (or not ) biopython
biopython
python
fasta
updated 4 months ago by
Mark
★ 1.5k • written 6.2 years ago by
juan.crescente
▴ 110
13
votes
7
replies
18k
views
Running STAR aligner on paired-end reads as single-end read
RNA-Seq
paired end
single end
STAR
align
updated 3 months ago by
xiaoleiusc
▴ 140 • written 5.6 years ago by
Glory Basumata
▴ 140
3
votes
8
replies
18k
views
Downloading gtf file for RefSeq
RNA-Seq
RefSeq
GTF
updated 11 weeks ago by
xiaoleiusc
▴ 140 • written 6.5 years ago by
KVC_bioinfo
▴ 590
19
votes
16
replies
18k
views
6 follow
Conversion of Gene Name to Ensembl ID
gene
RNA-Seq
R
genome
updated 4 months ago by
Nat.Nataren
▴ 10 • written 4.0 years ago by
bazok
▴ 10
51
votes
6
replies
18k
views
Decoy In Reference Assembly
1000genomes
updated 10 months ago by
kmzhou4
• 0 • written 10.8 years ago by
Sangwoo Kim
▴ 420
6
votes
5
replies
18k
views
7 follow
How different is rlog transformation from vst transformation in DESeq2
DESeq2
count normalization
updated 7 months ago by
ATpoint
81k • written 5.5 years ago by
piyushjo
▴ 700
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 4 weeks ago by
Alex Reynolds
35k • written 7.6 years ago by
bioinformatics.cancer
▴ 260
1
vote
2
replies
18k
views
Forum:
Would you rather analyze a dataset with a strong, non-collinear batch effect, or a weak, collinear batch effect.
collinear
latent
batch-effect
variable
GLM
8 months ago by
LauferVA
4.1k
17
votes
10
replies
18k
views
Regarding Split reads and discordant reads
genome
sequence
sequencing
alignment
updated 10 months ago by
Ram
43k • written 6.4 years ago by
DL
▴ 50
6
votes
9
replies
17k
views
HISAT2 software installation
RNA-Seq
updated 6 weeks ago by
GenoMax
140k • written 6.5 years ago by
saj98
▴ 140
21
votes
11
replies
17k
views
the problem with rpkm (and tpm)
RNA-Seq
next-gen
gene-expression
normalization
updated 9 months ago by
Chris
▴ 260 • written 9.5 years ago by
user123456
▴ 180
12
votes
11
replies
17k
views
Trying to get genome for bedtools
genome
updated 8 months ago by
mg
▴ 250 • written 7.6 years ago by
radwa.raed
▴ 40
8
votes
6
replies
17k
views
News:
Bioinformatics PhD Programs in the US
education
PhD
updated 10 months ago by
Ram
43k • written 6.3 years ago by
Ahmed Youssef
▴ 70
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
160k
9
votes
10
replies
17k
views
8 follow
Forum:
Open Source Bioinformatics projects for beginners
Open-Source
Beginners
updated 7 weeks ago by
Saransh
• 0 • written 6.2 years ago by
Eugenia84
▴ 40
17
votes
9
replies
17k
views
6 follow
Tool:
ggrepel: repel overlapping text labels in ggplot2
R
visualization
updated 9 months ago by
Ram
43k • written 8.2 years ago by
Kamil
★ 2.3k
48
votes
38
replies
17k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Eric Normandeau
11k
20
votes
10
replies
16k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 6 months ago by
Ram
43k • written 4.4 years ago by
WUSCHEL
▴ 750
12
votes
11
replies
16k
views
10 follow
Retrieve The Reads And Fastq From Bam File
samtools
updated 5 months ago by
Reem
• 0 • written 11.4 years ago by
rehma.ar
▴ 290
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 10 months ago by
GenoMax
140k • written 10.4 years ago by
Obi Griffith
20k
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 9 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
3
votes
9
replies
16k
views
8 follow
Module to RMSD two proteins with Python?
python
protein-structure
updated 9 months ago by
Aleksandr
• 0 • written 8.2 years ago by
bef1
• 0
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray
annotation
affymetrix
probeset
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Khader Shameer
18k
10
votes
8
replies
16k
views
6 follow
Error: Eof Marker Is Absent When Processing A Bam File
samtools
updated 10 months ago by
Ram
43k • written 11.6 years ago by
Mary
▴ 50
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 8 days ago by
Bionaught
• 0 • written 5.7 years ago by
firestar
★ 1.6k
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq
peak-calling
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Stew
★ 1.4k
7
votes
11
replies
16k
views
11 follow
How to generate KEGG pathway classification chart
RNA-Seq
kegg
updated 8 months ago by
microecologist93
▴ 20 • written 5.0 years ago by
dongchenchen
▴ 30
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 21 days ago by
barslmn
★ 2.1k • written 6.6 years ago by
a.rex
▴ 350
7
votes
14
replies
16k
views
7 follow
Tool:
Art: Simulation Tools To Generate Synthetic Next-Generation Sequencing Reads.
sequence
updated 9 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
21
votes
7
replies
15k
views
6 follow
GFA to Fasta file
sequence
updated 10 weeks ago by
Adam Taranto
▴ 40 • written 8.3 years ago by
marcela.uliano
▴ 90
15
votes
5
replies
15k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Obi Griffith
20k
67
votes
25
replies
15k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 5 months ago by
GenoMax
140k • written 5.1 years ago by
Phil Ewels
★ 1.4k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 9 months ago by
Ram
43k • written 7.6 years ago by
thomaskuilman
▴ 840
15
votes
11
replies
15k
views
10 follow
TCGA/Broad Institute CNV Files Segment Mean
tcga
cnv
updated 4 months ago by
sativus
▴ 20 • written 9.5 years ago by
dirigible2012
▴ 320
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 9 months ago by
Ram
43k • written 5.5 years ago by
Shahzad
▴ 30
1,000 results • Page
4 of 20
Recent Votes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
Answer: FDR and Bonferroni
Answer: FDR and Bonferroni
Answer: Choosing an FC Threshold
Answer: Choosing an FC Threshold
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Recent Replies
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
liuyibin2005
• 0
Dear all I have resepctively performed linear regression analyses on two idependent datasets. One is conducted on log2 transformed CPM f…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
• 0
you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
• 0
Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
Comment: Paired layout, but one fastq file
by
GenoMax
140k
There is a BAM file available here: https://sra-pub-src-2.s3.amazonaws.com/SRR14667226/CTRL_possorted_genome_bam.bam.1 Please get that wit…
Comment: Only one read per run - Trying to use CellRangerv7
by
dsull
★ 5.6k
1. This is a comment, not an answer. Please don't post it as an answer. :) 2. This is sci-rna-seq, not 10x rna-seq. CellRanger would not …
Comment: Only one read per run - Trying to use CellRangerv7
by
Sky
▴ 10
Sorry for the delayed reply. I have included my code and the output from downloading the four files. Each dataset only resulted in one fast…
Answer: FDR and Bonferroni
by
joe
▴ 470
> Any idea why this is happening? For example, I got 1064 significant > probes from raw p-values, but only 18 from Bonferroni correction, a…
Comment: Paired layout, but one fastq file
by
Sky
▴ 10
I am also having a similar issue where there is only one fastq file but no bam file available so from my understanding I can't use bamtofas…
Comment: convert cds to seurat object
by
sooni
▴ 20
Yes, I tried with `as.Seurat`. But there is an error follwing: Error: `No data in provided assay - logcounts`. How can I solve this problem?
Comment: novel and know mir156 and mir172
by
gayachit
▴ 200
Do you have RNAseq or small RNAseq data?
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