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12,524 results • Page
4 of 251
Sort: Votes
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Votes
Replies
38
votes
11
replies
4.1k
views
7 follow
Python Documentation Tools
python
updated 11 months ago by
Ram
43k • written 14.0 years ago by
Thaman
★ 3.3k
38
votes
17
replies
3.3k
views
7 follow
Forum:
Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam
bam
samtools
updated 11 months ago by
Ram
43k • written 3.7 years ago by
kojix2
▴ 250
38
votes
8
replies
1.7k
views
6 follow
News:
What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq
DNA
WGS
updated 11 months ago by
Alex Reynolds
35k • written 11 months ago by
David Langenberger
11k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 21 days ago by
noodle
▴ 580
38
votes
7
replies
2.3k
views
News:
2 last seats available - 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Transcriptomics
DNA-Seq
Variant-Calling
RNA-Seq
9 months ago by
David Langenberger
11k
38
votes
14
replies
9.1k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl
python
biopython
genome
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Rvidal
▴ 270
37
votes
9
replies
4.5k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference
GRCh38
t2t
calling
variant
updated 11 months ago by
LauferVA
4.2k • written 13 months ago by
onter
▴ 170
37
votes
11
replies
33k
views
6 follow
Sjdboverhang Option In Star
updated 10 months ago by
Kermit
▴ 90 • written 10.2 years ago by
Martombo
★ 3.1k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 8 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
37
votes
20
replies
7.3k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
37
votes
5
replies
14k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 5 weeks ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
36
votes
34
replies
2.9k
views
9 follow
Forum:
New to bioinformatics.....
gene
updated 12 months ago by
Ram
43k • written 6.2 years ago by
sms.00196
• 0
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 5 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome
Assembly
sequence
blast
updated 10 months ago by
Kermit
▴ 90 • written 8.6 years ago by
liuyifan2014
▴ 110
36
votes
17
replies
3.7k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
36
votes
13
replies
7.3k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data
galaxy
written 13.0 years ago by
Pi
▴ 520
35
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam
RNA-seq
updated 4 months ago by
Ram
43k • written 12.0 years ago by
snakesgun
▴ 160
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 7 months ago by
ashotmarg2004
▴ 130 • written 7.9 years ago by
William
★ 5.3k
35
votes
15
replies
12k
views
10 follow
How to select an aligner?
RNA-Seq
next-gen
alignment
updated 4 months ago by
Erfan
• 0 • written 6.0 years ago by
marongiu.luigi
▴ 710
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq
peak-calling
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Stew
★ 1.4k
34
votes
23
replies
22k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 8 months ago by
alejandrogzi
▴ 120 • written 6.1 years ago by
JJ
▴ 680
34
votes
9
replies
11k
views
7 follow
Tool:
Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by
Ram
43k • written 10.2 years ago by
brentp
24k
34
votes
8
replies
2.7k
views
9 follow
Forum:
Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a master of none? How can your CV reflect the diverse skills that you have …
cv
industry
career
updated 11 months ago by
Ram
43k • written 4.6 years ago by
'
▴ 300
34
votes
22
replies
3.0k
views
11 follow
Forum:
Have we failed as bioinformatician in this time of COVID-19
Bioinformatician
COVID-19
updated 11 months ago by
Ram
43k • written 4.0 years ago by
heididunst
▴ 10
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 29 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 10 months ago by
Ram
43k • written 11.0 years ago by
hicsuntdrac0nis
▴ 250
33
votes
23
replies
4.3k
views
8 follow
Forum:
Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF
file-format
genomics
updated 11 months ago by
Jeremy Leipzig
22k • written 11 months ago by
LauferVA
4.2k
33
votes
9
replies
10k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing
fastq
c
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Jeremy Leipzig
22k
33
votes
10
replies
36k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 10 months ago by
Ram
43k • written 9.9 years ago by
pwg46
▴ 540
33
votes
3
replies
15k
views
Tool:
Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa
ngs
updated 10 months ago by
Ram
43k • written 11.2 years ago by
lh3
33k
33
votes
12
replies
1.1k
views
7 follow
Forum:
Nextflow and self-made pipelines opinion
nextflow
pipeline
data-analysis
11 weeks ago by
karlaarz
▴ 110
32
votes
4
replies
9.4k
views
Fastq Qualities For Solexa/Illumina
sequencing-quality
next-gen-sequencing
fastq
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
32
votes
13
replies
10.0k
views
11 follow
Any Recommendations For Statistical Genetics Texts?
genetics
statistics
gwas
updated 4 months ago by
Angelo
• 0 • written 13.8 years ago by
Shigeta
▴ 180
31
votes
14
replies
24k
views
7 follow
Difference between tSNE and PCA analysis
next-gen
rna-seq
updated 12 weeks ago by
Jeremy Leipzig
22k • written 6.3 years ago by
Qingyang Xiao
▴ 160
31
votes
22
replies
13k
views
6 follow
Tool:
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ
SeqKit
FASTA
updated 11 months ago by
Ram
43k • written 7.6 years ago by
shenwei356
8.5k
31
votes
41
replies
2.8k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 11 months ago by
Ram
43k • written 4.2 years ago by
K.Gee
▴ 40
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 11 months ago by
Ram
43k • written 6.0 years ago by
Jennifer Pham
▴ 450
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 4 months ago by
gernophil
▴ 80 • written 12.4 years ago by
Preethi
▴ 110
31
votes
11
replies
6.7k
views
8 follow
Basics Of Systems Biology...
network
updated 10 months ago by
bryan.smith4756
• 0 • written 13.8 years ago by
pixie@bioinfo
★ 1.5k
31
votes
11
replies
5.7k
views
6 follow
Assessing Cluster Reliability/Stability In Microarray Experiments
clustering
microarray
gene
updated 6 months ago by
Ram
43k • written 14.1 years ago by
toni
★ 2.2k
31
votes
16
replies
2.2k
views
8 follow
Forum:
What is in your opinion the current state-of-the-art sequencing platform for genomic assembly (Nov 2019)
next-gen-sequencing
assembly
genome
updated 11 months ago by
Ram
43k • written 4.6 years ago by
Antonio R. Franco
★ 5.1k
31
votes
8
replies
13k
views
Experiences With Clc Genomics Workbench (Or Other Commercial Tools) For Next-Gen Sequencing
next-gen-sequencing
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Istvan Albert
100k
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 7 weeks ago by
Ram
43k • written 13.6 years ago by
toshnam
▴ 650
31
votes
8
replies
8.3k
views
9 follow
Notepad and word will not read Fastq or FASTA files
software-error
fastq
written 9.2 years ago by
paul.sillence
• 0
30
votes
13
replies
3.7k
views
11 follow
Forum:
what is your daily must see bioinformatics web site?
learn
technology
updated 11 months ago by
Ram
43k • written 9.7 years ago by
Medhat
9.7k
30
votes
15
replies
10k
views
7 follow
Tool:
Snakemake--Python-Based Workflow Management
workflow
snakemake
python
updated 11 months ago by
Ram
43k • written 10.5 years ago by
Sean Davis
26k
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books
online
updated 6 months ago by
Ram
43k • written 14.1 years ago by
hadasa
★ 1.0k
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 6 months ago by
Ram
43k • written 14.2 years ago by
Khader Shameer
18k
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 4 weeks ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
12,524 results • Page
4 of 251
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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