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Limit : this year
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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
40
votes
23
replies
4.1k
views
12 follow
Forum:
Why learn programming in bioinformatics?
Programming
updated 11 months ago by
Ram
43k • written 5.6 years ago by
joselu
▴ 110
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
39
votes
15
replies
23k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene
r
updated 5 months ago by
Ram
43k • written 14.1 years ago by
John
▴ 790
39
votes
21
replies
13k
views
10 follow
Forum:
Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
Juke34
8.5k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
12 weeks ago by
Jeremy Leipzig
22k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 9 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
39
votes
11
replies
9.1k
views
11 follow
Where Can I Get The Secondary Structure Of A Protein?
protein
structure
sequence
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
39
votes
18
replies
6.0k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Heather Piwowar
▴ 380
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
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
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 8 weeks ago by
Alex Reynolds
35k • written 7.7 years ago by
bioinformatics.cancer
▴ 260
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 10 months ago by
Ram
43k • written 8.1 years ago by
jgbaum
▴ 140
38
votes
14
replies
9.0k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl
python
biopython
genome
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Rvidal
▴ 270
38
votes
26
replies
18k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
38
votes
17
replies
3.2k
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 10 months ago by
Ram
43k • written 3.7 years ago by
kojix2
▴ 250
38
votes
8
replies
1.6k
views
6 follow
News:
What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq
DNA
WGS
updated 10 months ago by
Alex Reynolds
35k • written 10 months ago by
David Langenberger
11k
38
votes
25
replies
9.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 7 months ago by
Ram
43k • written 8.1 years ago by
waqasnayab
▴ 250
38
votes
11
replies
4.1k
views
7 follow
Python Documentation Tools
python
updated 10 months ago by
Ram
43k • written 13.9 years ago by
Thaman
★ 3.3k
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 16 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
37
votes
9
replies
4.4k
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 12 months ago by
onter
▴ 170
37
votes
16
replies
4.0k
views
9 follow
Forum:
Sanger sequencing is no longer the gold standard?
Sanger
NGS
updated 11 months ago by
Ram
43k • written 6.5 years ago by
lamteva.vera
▴ 220
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome
Assembly
sequence
blast
updated 9 months ago by
Kermit
▴ 90 • written 8.6 years ago by
liuyifan2014
▴ 110
36
votes
34
replies
2.8k
views
9 follow
Forum:
New to bioinformatics.....
gene
updated 11 months ago by
Ram
43k • written 6.1 years ago by
sms.00196
• 0
36
votes
39
replies
4.1k
views
11 follow
Forum:
Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast
RNA-Seq
alignment
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 6.5 years ago by
dhbradshaw
▴ 130
36
votes
17
replies
3.7k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 4 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
36
votes
11
replies
33k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by
Kermit
▴ 90 • written 10.2 years ago by
Martombo
★ 3.1k
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 12.9 years ago by
Pi
▴ 520
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 11 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
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 5.9 years ago by
marongiu.luigi
▴ 710
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 6 months ago by
ashotmarg2004
▴ 130 • written 7.8 years ago by
William
★ 5.3k
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq
peak-calling
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Stew
★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 7 days ago by
Hagen
▴ 10 • written 10.2 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 5 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
34
votes
22
replies
2.9k
views
11 follow
Forum:
Have we failed as bioinformatician in this time of COVID-19
Bioinformatician
COVID-19
updated 10 months ago by
Ram
43k • written 4.0 years ago by
heididunst
▴ 10
34
votes
5
replies
2.3k
views
Forum:
what we should reply when we are asked do you have any question?
career
interview
updated 11 months ago by
Ram
43k • written 6.9 years ago by
zizigolu
★ 4.3k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 9 months ago by
Ram
43k • written 10.9 years ago by
hicsuntdrac0nis
▴ 250
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 10 months ago by
Ram
43k • written 4.5 years ago by
'
▴ 300
34
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 11.9 years ago by
snakesgun
▴ 160
33
votes
23
replies
4.1k
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 10 months ago by
Jeremy Leipzig
22k • written 10 months ago by
LauferVA
4.2k
33
votes
23
replies
21k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 7 months ago by
alejandrogzi
▴ 120 • written 6.1 years ago by
JJ
▴ 680
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 9 months ago by
Ram
43k • written 9.8 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 11.1 years ago by
lh3
33k
33
votes
9
replies
10k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing
fastq
c
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Jeremy Leipzig
22k
32
votes
13
replies
9.9k
views
11 follow
Any Recommendations For Statistical Genetics Texts?
genetics
statistics
gwas
updated 4 months ago by
Angelo
• 0 • written 13.7 years ago by
Shigeta
▴ 180
1,000 results • Page
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Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
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Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
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Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
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▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
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![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
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141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
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19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
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The_PyPanda
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Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
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You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
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ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
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If you have the accession numbers can you not use something like `eutils`?
Comment: Create a new bed file with all pairwise combinations between two other bed files
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161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
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by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
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