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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
115
votes
66
replies
39k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
ENA
fastq-dump
Tutorial
Fastq
7 months ago by
ATpoint
68k
115
votes
25
replies
32k
views
20 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 16 days ago by
Ram
37k • written 7.7 years ago by
mhockin
▴ 600
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 days ago by
Ram
37k • written 8.6 years ago by
kay
▴ 320
112
votes
24
replies
44k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 5 months ago by
Ram
37k • written 11.7 years ago by
Matthieu
▴ 480
109
votes
56
replies
39k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq
next-gen
sequencing
fusion
updated 4 months ago by
Ram
37k • written 10.7 years ago by
KS
▴ 380
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by
aswinssoman
▴ 20 • written 10.5 years ago by
Mchimich
▴ 320
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 4 months ago by
Ram
37k • written 10.1 years ago by
henryvuong
▴ 810
103
votes
12
replies
70k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 3 months ago by
Ram
37k • written 11.3 years ago by
Bioscientist
★ 1.7k
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
tool
updated 7 months ago by
Ram
37k • written 12.9 years ago by
Biostar User
★ 1.0k
100
votes
81
replies
23k
views
17 follow
Duplicates on Illumina
duplicates
illumina
updated 5 months ago by
GenoMax
125k • written 6.1 years ago by
predeus
★ 1.8k
99
votes
36
replies
27k
views
32 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 12 days ago by
Jeremy Leipzig
21k • written 9.2 years ago by
14134125465346445
★ 3.6k
98
votes
16
replies
29k
views
18 follow
Tutorial:
Heatmaps in R
Tutorial
R
heatmap
9 months ago by
Jean-Karim Heriche
26k
98
votes
14
replies
95k
views
14 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 10 months ago by
Juke34
7.5k • written 10.7 years ago by
GouthamAtla
12k
97
votes
9
replies
111k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 9 months ago by
henry-keen
▴ 40 • written 9.4 years ago by
newDNASeqer
▴ 750
97
votes
19
replies
86k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 5 months ago by
Ram
37k • written 13.0 years ago by
Giovanni M Dall'Olio
27k
97
votes
31
replies
80k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 6 months ago by
Ram
37k • written 11.6 years ago by
2184687-1231-83-
★ 5.0k
97
votes
23
replies
32k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa
tophat
rna-seq
updated 8 months ago by
Ram
37k • written 10.1 years ago by
Lisa
▴ 330
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 5 days ago by
Ram
37k • written 10.4 years ago by
Istvan Albert
96k
94
votes
31
replies
36k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python
alignment
next-gen
sequencing
database
updated 10 months ago by
Ram
37k • written 12.5 years ago by
User 1586
▴ 280
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 11 months ago by
Dan
▴ 60 • written 10.7 years ago by
GPR
▴ 380
93
votes
19
replies
55k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree
tool
phylogenetics
viewer
updated 8 months ago by
Theo
▴ 20 • written 12.4 years ago by
Niek De Klein
★ 2.6k
92
votes
105
replies
32k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 4 days ago by
s.w.vanderlaan
▴ 40 • written 4.4 years ago by
Kevin Blighe
84k
92
votes
24
replies
72k
views
19 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 12 months ago by
ashotmarg2004
▴ 120 • written 10.7 years ago by
Rubal7
▴ 820
92
votes
20
replies
27k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r
visualization
updated 8 months ago by
Ram
37k • written 11.0 years ago by
John
★ 1.5k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks
selection
software
updated 5 months ago by
Michael Dondrup
52k • written 12.0 years ago by
Jarretinha
3.4k
91
votes
20
replies
18k
views
15 follow
Forum:
Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one
WGS
RNA-Seq
next-gen
Exome
updated 3 months ago by
Ram
37k • written 8.7 years ago by
Obi Griffith
20k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by
Ram
37k • written 11.8 years ago by
Ryan D
★ 3.4k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification
microarray
expression
bioconductor
Tutorial
updated 4 months ago by
Ram
37k • written 9.3 years ago by
Obi Griffith
20k
89
votes
38
replies
124k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by
Wang Cong
▴ 10 • written 10.6 years ago by
abi
▴ 370
89
votes
31
replies
11k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs
visualization
genomics
updated 6 months ago by
Ram
37k • written 10.9 years ago by
John
★ 1.5k
88
votes
32
replies
8.1k
views
11 follow
Forum:
Vintage / unconventional pictures for Bioinformatics
history
picture
updated 10 months ago by
Ram
37k • written 8.3 years ago by
Pierre Lindenbaum
152k
87
votes
16
replies
19k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat
batch-effect
sva
updated 6 days ago by
madbadradscientist
▴ 20 • written 7.7 years ago by
Christian
★ 3.0k
87
votes
37
replies
47k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 11 months ago by
Ram
37k • written 9.5 years ago by
Hunter
▴ 110
87
votes
18
replies
56k
views
12 follow
Sequence length from Fasta
fasta
updated 6 weeks ago by
Ram
37k • written 8.2 years ago by
bongbang
▴ 80
85
votes
19
replies
38k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly
quality
next-gen
updated 12 months ago by
WANG
▴ 10 • written 10.0 years ago by
diltsjeri
▴ 470
84
votes
36
replies
16k
views
13 follow
Forum:
Benchmark - Comparison of Different NGS Mappers
mRNA-Seq
benchmark
NGS-mapper
updated 10 months ago by
Ram
37k • written 8.1 years ago by
David Langenberger
9.8k
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
R
pathway
enrichment
active subnetwork
Tutorial
updated 6 months ago by
Ram
37k • written 4.6 years ago by
egeulgen
★ 1.3k
83
votes
16
replies
82k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 10 weeks ago by
bhanu.chandra1
▴ 50 • written 7.8 years ago by
Prakki Rama
★ 2.6k
83
votes
30
replies
5.4k
views
18 follow
Forum:
Optimal design for bioinformatics "lab" space?
design
lab-space
updated 7 months ago by
Ram
37k • written 7.8 years ago by
Casey Bergman
18k
82
votes
28
replies
27k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR
BioConductor
R
Graphics
Tutorial
updated 12 weeks ago by
GenoMax
125k • written 6.9 years ago by
Obi Griffith
20k
81
votes
8
replies
7.7k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
genomics
workshop
Tutorial
lectures
training
updated 9 months ago by
Ram
37k • written 8.7 years ago by
Malachi Griffith
19k
81
votes
23
replies
11k
views
10 follow
Transform A Pipeline Of R Scripts Into A Web Application
webservice
web
pipeline
galaxy
updated 9 months ago by
Ram
37k • written 12.5 years ago by
Giovanni M Dall'Olio
27k
81
votes
21
replies
4.0k
views
16 follow
Forum:
[UPDATE] Thrown into a Bioinformatics Position
beginner
help
updated 5 months ago by
Ram
37k • written 6.6 years ago by
Sinji
★ 3.2k
80
votes
34
replies
3.9k
views
11 follow
Forum:
Authorship issues- how to resolve?
authorship
updated 4 weeks ago by
Ram
37k • written 7.7 years ago by
datanerd
▴ 500
79
votes
21
replies
13k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
Tutorial
GSEA
RNA-Seq
7 weeks ago by
Hamid Ghaedi
2.8k
79
votes
22
replies
79k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 10 weeks ago by
Ram
37k • written 11.3 years ago by
Hamilton
▴ 290
78
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 9.6 years ago by
Eric Normandeau
11k
78
votes
41
replies
27k
views
24 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 10 weeks ago by
Acadia
• 0 • written 9.3 years ago by
Irsan
★ 7.6k
78
votes
6
replies
40k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam
samtools
next-gen
updated 10 months ago by
Ram
37k • written 10.8 years ago by
Stefano Berri
4.3k
77
votes
8
replies
11k
views
13 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes
visualizations
rearrangements
updated 4 months ago by
Ram
37k • written 7.4 years ago by
stianlagstad
★ 1.1k
1,000 results • Page
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Filtering out samples by FORMAT attributes using bcftools
Deseq2 with one factor and multiple levels
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Gene Expression Omnibus Data Mining (IA): Quick and easy download of GEO data
SNP calling
Comment: Annotating ENS codes to gene name
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Comment: ceres score in crispr screen
by
edus_bioinfo
▴ 20
they didnt provide a good tutorial thats why i cannot determine whether i have problem in input files ps: but i cannot run the demo files
Comment: ceres score in crispr screen
by
edus_bioinfo
▴ 20
:) technical support. > my run is giving Error: Encountered internal Bowtie 2 exception (#1) Command: /Users/sudeeris/Downloads/bowtie2-…
Comment: Network analysis for two Factors
by
seidel
10k
Have you looked at any tutorials? Three are many out there. ([1][1], [2][2], [3][3], [etc.][4]) Do you have a preferred language? [1]: …
Comment: ceres score in crispr screen
by
seidel
10k
Are you looking for moral support or technical support? Have you tried using it with an older version of R and bioconductor? (i.e. circa 20…
Comment: PLINK2 selecting variants based on INFO score
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chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
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Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me wget https://anaconda.org/…
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by
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★ 5.4k
First issue is that GEO series matrix files can't be read using `read.delim`. Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
m.c.roozen
• 0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
Answer: samtools markdup in Rsamtools
by
joe
▴ 350
You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
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by
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152k
> But other solutions are also fine: bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
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68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
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Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
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9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
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