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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
238
votes
176
replies
85k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 days ago by
Ram
39k • written 7.8 years ago by
TriS
★ 4.6k
95
votes
27
replies
77k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 16 days ago by
NIRJHAR
• 0 • written 11.0 years ago by
Rubal7
▴ 820
160
votes
63
replies
76k
views
38 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 4 days ago by
Ram
39k • written 12.2 years ago by
Ketil
4.1k
129
votes
22
replies
52k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 12 hours ago by
Kevin Blighe
85k • written 5.5 years ago by
Mike
★ 1.8k
1.2k
votes
206
replies
50k
views
108 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 days ago by
Raony Guimarães
★ 1.2k • written 12.2 years ago by
Jeremy Leipzig
21k
66
votes
19
replies
47k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
tools
updated 5 days ago by
Sara
▴ 10 • written 10.3 years ago by
14134125465346445
★ 3.6k
115
votes
35
replies
38k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 23 days ago by
Ram
39k • written 6.0 years ago by
ropolocan
▴ 760
34
votes
13
replies
37k
views
8 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 7 days ago by
Kermit
▴ 80 • written 6.9 years ago by
William
★ 5.2k
120
votes
33
replies
36k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 27 days ago by
carlopecoraro2
★ 2.3k • written 9.8 years ago by
Eric Normandeau
11k
67
votes
15
replies
32k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 18 days ago by
Ram
39k • written 13.0 years ago by
brentp
24k
20
votes
9
replies
30k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 29 days ago by
Kevin Blighe
85k • written 10.9 years ago by
sthait
▴ 120
6
votes
25
replies
29k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 5 days ago by
13554221497
• 0 • written 5.2 years ago by
ARich
▴ 130
78
votes
42
replies
29k
views
25 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 27 days ago by
Ram
39k • written 9.6 years ago by
Irsan
★ 7.7k
100
votes
38
replies
28k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 27 days ago by
Jeremy Leipzig
21k • written 9.6 years ago by
14134125465346445
★ 3.6k
19
votes
9
replies
27k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 18 days ago by
Ram
39k • written 5.6 years ago by
Arindam Ghosh
▴ 500
6
votes
23
replies
25k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github
R
phylogeny
devtools
updated 5 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
13
votes
3
replies
25k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 4 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
27
votes
17
replies
20k
views
8 follow
BioPython: convert fasta to fastq without quality score input file
parsing
phred
fasta
BioPython
fastq
updated 3 days ago by
capemaster
• 0 • written 9.1 years ago by
Josh Herr
5.7k
8
votes
6
replies
19k
views
6 follow
Subsetting a fasta file using seqinr in R
sequence
R
fasta
updated 14 days ago by
GenoMax
129k • written 8.4 years ago by
henrikkjeldal
▴ 10
28
votes
11
replies
18k
views
9 follow
Salary For A Bioinformatics Programmer In Europe?
career
updated 12 days ago by
Ram
39k • written 11.8 years ago by
Jeroen Van Goey
2.3k
0
votes
1
reply
17k
views
What is positives when I blast two sequences?
identity
blast
NCBI
updated 16 days ago by
Ram
39k • written 5.3 years ago by
vincent.bioscience
• 0
39
votes
6
replies
17k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 19 days ago by
Ram
39k • written 5.8 years ago by
steve
★ 3.3k
8
votes
6
replies
16k
views
News:
Bioinformatics PhD Programs in the US
education
PhD
updated 18 days ago by
Ram
39k • written 5.5 years ago by
Ahmed Youssef
▴ 70
48
votes
6
replies
16k
views
Decoy In Reference Assembly
1000genomes
updated 18 days ago by
kmzhou4
• 0 • written 10.0 years ago by
Sangwoo Kim
▴ 420
83
votes
34
replies
16k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 9 days ago by
adelheidkratzer
• 0 • written 5.0 years ago by
egeulgen
★ 1.3k
16
votes
10
replies
15k
views
Regarding Split reads and discordant reads
genome
sequence
sequencing
alignment
updated 18 days ago by
Ram
39k • written 5.6 years ago by
DL
▴ 40
9
votes
9
replies
15k
views
6 follow
Forum:
Open Source Bioinformatics projects for beginners
Open-Source
Beginners
updated 17 days ago by
Ram
39k • written 5.4 years ago by
Eugenia84
▴ 40
11
votes
7
replies
13k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 19 days ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
5
votes
4
replies
13k
views
How to calculate the Position Weight Matrix score?
pssm
pwm
updated 24 days ago by
Ram
39k • written 6.2 years ago by
jordidebruin
• 0
10
votes
8
replies
13k
views
6 follow
Error: Eof Marker Is Absent When Processing A Bam File
samtools
updated 24 days ago by
Ram
39k • written 10.8 years ago by
Mary
▴ 50
21
votes
7
replies
13k
views
Use samtools index on multiple bam files at the same time from the command line?
RNA-Seq
next-gen
sequence
updated 28 days ago by
Pierre Lindenbaum
154k • written 7.5 years ago by
nash.claire
▴ 470
4
votes
5
replies
13k
views
Take A Subset Of A Fastq Paired-End Sample
paired-end
fastq
rna-seq
illumina
updated 4 days ago by
Ram
39k • written 10.2 years ago by
dfernan
▴ 730
3
votes
4
replies
12k
views
Python bioinformatics mini project ideas
programming
python
project
updated 16 days ago by
Ram
39k • written 5.3 years ago by
Galaxy123
▴ 20
59
votes
15
replies
12k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 10 days ago by
Ram
39k • written 4.7 years ago by
finswimmer
16k
25
votes
22
replies
11k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 16 days ago by
Ram
39k • written 6.3 years ago by
Brian Bushnell
18k
9
votes
15
replies
11k
views
10 follow
Error In Bedtools Getfasta: Chromosome Not Found
bedtools
updated 23 days ago by
Ram
39k • written 10.3 years ago by
Pat Baldrich
▴ 10
9
votes
31
replies
11k
views
6 follow
How to concatenate multiple fasta file
sequence
genome
updated 4 days ago by
doggie
• 0 • written 4.8 years ago by
fec2
▴ 40
3
votes
3
replies
11k
views
RAxML outputs: which one I have to take ?
RAxML output
updated 28 days ago by
Michael
52k • written 6.5 years ago by
Picasa
▴ 640
12
votes
3
replies
11k
views
words: time course VS time series
time-course
time-series
updated 5 days ago by
Ram
39k • written 7.7 years ago by
pengchy
▴ 450
37
votes
21
replies
10k
views
10 follow
Forum:
Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 10 days ago by
Ram
39k • written 4.6 years ago by
Juke34
7.9k
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 5 days ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
1
vote
4
replies
9.8k
views
Error in RStudioGD() : Shadow graphics device error: r error 4 (R code execution error)
Rstudio
updated 18 days ago by
Ram
39k • written 5.6 years ago by
Grunir112
▴ 10
16
votes
9
replies
9.7k
views
6 follow
problems with MAF for MutSigCV (vcf2maf)
vcf2maf
snp
vcf
MutSigCV
gatk
updated 7 days ago by
RAJDEEP
• 0 • written 8.8 years ago by
A. Domingues
★ 2.6k
26
votes
9
replies
8.9k
views
6 follow
DESeq2 modelling and Wald's test
RNA-Seq
DESeq2
updated 10 days ago by
Picasa
▴ 640 • written 5.2 years ago by
bioinfo456
▴ 150
9
votes
23
replies
8.6k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 17 days ago by
Ram
39k • written 5.4 years ago by
vimalkvn
▴ 310
1
vote
11
replies
8.5k
views
6 follow
Truncated sam file - Parse error
sam
bam
BWA
updated 11 days ago by
ATpoint
72k • written 5.8 years ago by
fiona.newberry
▴ 80
0
votes
0
replies
8.5k
views
News:
2nd edition: Population Genomics course in Berlin. May 14-18 2018
Population-Genomics
Plink
R
VCFtools
updated 18 days ago by
Ram
39k • written 5.7 years ago by
carlopecoraro2
★ 2.3k
11
votes
8
replies
8.3k
views
9 follow
Genome assembly statistical tools
statistics
tools
Assembly
updated 3 days ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
10
votes
8
replies
8.3k
views
7 follow
Building Dict File for GATK
java
gatk
updated 4 days ago by
dare_devil
★ 3.1k • written 3.4 years ago by
dec986
▴ 360
13
votes
7
replies
8.2k
views
Forum:
The struggle between fastq and fastq.gz, compressed v/s uncompressed file formats
fastq
updated 23 days ago by
Ram
39k • written 5.9 years ago by
lakhujanivijay
5.7k
1,000 results • Page
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Recent Votes
C: parsing fasta file
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
A: ggplot2 labeling and coloring specific Data points in Scatter Plot
Answer: How to sort gff3 according to chromosome order?
Answer: how to sort unique seq from fasta files
Answer: Make a BedGraph file
Answer: Finding Enhancers using Genomation library
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Recent Replies
Comment: Alignment of case vs. control from different origin
by
sativus
• 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis
by
nux
▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error
by
bestone
▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
• 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation"
by
bioinfo_ga
▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output
by
bioinfo_ga
▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file
by
kirillkirilenko
▴ 10
It works, thank you!
Comment: CNNScoreVariants Error
by
Pierre Lindenbaum
154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
Cathal
• 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/ Since a single CpG has a length o…
Comment: Gene enrichment analysis
by
ATpoint
72k
I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.
Answer: Finding Enhancers using Genomation library
by
ATpoint
72k
You cannot derive enhancers from methylation profiles. Enhancers are regulatory elements, and they either are methylated or not. There is l…
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