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1,000 results • Page
3 of 20
Sort: Votes
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Views
Votes
Replies
86
votes
29
replies
8.7k
views
9 follow
Forum:
What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU
brexit
EBI
politics
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
Michael
52k
84
votes
16
replies
86k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 6 months ago by
bhanu.chandra1
▴ 50 • written 8.1 years ago by
Prakki Rama
★ 2.6k
84
votes
22
replies
3.7k
views
12 follow
Forum:
is fortran still used in bioinformatics?
FORTRAN
R
updated 12 weeks ago by
Ram
39k • written 4.0 years ago by
Manoj
▴ 180
83
votes
34
replies
16k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 7 days ago by
adelheidkratzer
• 0 • written 4.9 years ago by
egeulgen
★ 1.3k
83
votes
21
replies
16k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 weeks ago by
Ram
39k • written 2.6 years ago by
Hamid Ghaedi
2.9k
83
votes
30
replies
5.7k
views
18 follow
Forum:
Optimal design for bioinformatics "lab" space?
design
lab-space
updated 11 months ago by
Ram
39k • written 8.1 years ago by
Casey Bergman
18k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 3 months ago by
Ram
39k • written 7.2 years ago by
Obi Griffith
20k
82
votes
32
replies
6.6k
views
13 follow
Forum:
Shall We Go Back To Stackexchange?
meta
updated 3 months ago by
Ram
39k • written 10.5 years ago by
14134125465346445
★ 3.6k
82
votes
19
replies
12k
views
8 follow
Future Directions In Bioinformatics
subjective
career
updated 3 months ago by
Ram
39k • written 12.5 years ago by
Hranjeev
★ 1.5k
82
votes
21
replies
74k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
cmdcolin
★ 3.0k • written 4.9 years ago by
otwtgin2010
▴ 540
81
votes
8
replies
8.0k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 12 weeks ago by
Ram
39k • written 9.0 years ago by
Malachi Griffith
19k
81
votes
39
replies
6.2k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 3 months ago by
Ram
39k • written 10.4 years ago by
Istvan Albert
98k
81
votes
21
replies
4.2k
views
16 follow
Forum:
[UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 11 weeks ago by
Ram
39k • written 7.0 years ago by
Sinji
★ 3.2k
80
votes
2
replies
54k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by
Ram
39k • written 9.9 years ago by
Eric Normandeau
11k
80
votes
23
replies
4.5k
views
11 follow
Forum:
Are we facing a bioinformatician shortage?
salary
career
updated 12 weeks ago by
Ram
39k • written 8.6 years ago by
Christian
★ 3.0k
80
votes
34
replies
4.1k
views
11 follow
Forum:
Authorship issues- how to resolve?
authorship
updated 4 months ago by
Ram
39k • written 8.0 years ago by
datanerd
▴ 520
79
votes
22
replies
83k
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 6 months ago by
Ram
39k • written 11.6 years ago by
Hamilton
▴ 290
79
votes
35
replies
8.1k
views
17 follow
Forum:
Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship
career
updated 5 days ago by
jli.ww
• 0 • written 7.5 years ago by
sentausa
▴ 650
78
votes
42
replies
29k
views
25 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 25 days ago by
Ram
39k • written 9.6 years ago by
Irsan
★ 7.7k
78
votes
31
replies
5.8k
views
14 follow
Forum:
Do Bad Questions Even Exist?
biostars
general
education
updated 3 months ago by
Ram
39k • written 12.3 years ago by
Chris Evelo
10k
77
votes
8
replies
12k
views
13 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes
visualizations
rearrangements
updated 8 months ago by
Ram
39k • written 7.7 years ago by
stianlagstad
★ 1.1k
77
votes
18
replies
44k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 10 months ago by
Dan
• 0 • written 13.0 years ago by
Science_Robot
★ 1.1k
77
votes
22
replies
21k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly
next-gen
updated 8 months ago by
Ram
39k • written 11.0 years ago by
Prakki Rama
★ 2.6k
77
votes
27
replies
50k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 9 months ago by
Johan Zicola
▴ 70 • written 9.5 years ago by
Ram
▴ 180
76
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 11 weeks ago by
Ram
39k • written 5.3 years ago by
Kevin Blighe
85k
76
votes
35
replies
26k
views
13 follow
Illumina Instrument Type from fastq?
fastq
updated 4 weeks ago by
Nathan
▴ 20 • written 6.9 years ago by
andrew.j.skelton73
6.5k
76
votes
86
replies
26k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression
bbmap
clumpify
pigz
storage
Tool
updated 5 months ago by
GenoMax
129k • written 6.5 years ago by
Brian Bushnell
18k
75
votes
22
replies
50k
views
17 follow
How To Download All Sra Samples At Once ?
geo
sra
updated 10 weeks ago by
Ram
39k • written 9.3 years ago by
biorepine
★ 1.5k
74
votes
24
replies
54k
views
16 follow
How To Sort Bed Format File
bed
updated 7 months ago by
Pierre Lindenbaum
154k • written 10.3 years ago by
lyz10302012
▴ 430
74
votes
14
replies
28k
views
12 follow
Forum:
Bioinformatics Consulting Thoughts
consulting
updated 11 months ago by
Ram
39k • written 13.0 years ago by
Will
4.5k
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 7 months ago by
Ram
39k • written 9.5 years ago by
Nicholas Spies
★ 1.2k
73
votes
25
replies
102k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 11 months ago by
Ram
39k • written 8.1 years ago by
Chenglin
▴ 250
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 3 months ago by
Ram
39k • written 10.0 years ago by
Medhat
9.6k
72
votes
18
replies
6.8k
views
17 follow
Forum:
What Is One Book Every Bioinformatician Should Read?
books
updated 3 months ago by
Ram
39k • written 9.9 years ago by
Philipp Bayer
7.8k
72
votes
20
replies
24k
views
11 follow
Parsing Ncbi Taxonomic Tree?
ncbi
taxonomy
python
tree
updated 5 months ago by
Ram
39k • written 11.6 years ago by
Prohan
▴ 350
72
votes
60
replies
24k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 3 months ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
72
votes
28
replies
5.4k
views
10 follow
Forum:
Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services
ethics
misconduct
updated 11 months ago by
Ram
39k • written 8.4 years ago by
Angle45
▴ 90
72
votes
12
replies
3.8k
views
7 follow
Does Pre-Publishing Open Source Algorithms Hurt Chances Of Getting Published?
publication
algorithm
updated 10 months ago by
Ram
39k • written 11.7 years ago by
Martijn Van Iersel
▴ 570
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 3 months ago by
Ram
39k • written 10.3 years ago by
lh3
33k
72
votes
48
replies
7.1k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 3 months ago by
Ram
39k • written 12.1 years ago by
User 59
13k
71
votes
71
replies
25k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot
ggplot2
ggrepel
bioconductor
Tool
updated 7 months ago by
hermidalc
▴ 40 • written 4.8 years ago by
Kevin Blighe
85k
71
votes
17
replies
32k
views
14 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 4 months ago by
Ming Tommy Tang
★ 2.9k • written 9.1 years ago by
M K
▴ 600
70
votes
19
replies
4.7k
views
13 follow
Forum:
Thrown Into A Bioinformatics Position
computational-analysis
updated 10 months ago by
Ram
39k • written 7.7 years ago by
System
▴ 170
70
votes
16
replies
9.1k
views
11 follow
Creating A New Bioinformatics Unit
core
career
updated 3 months ago by
Ram
39k • written 11.9 years ago by
Israel Barrantes
▴ 790
70
votes
26
replies
25k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by
Ram
39k • written 9.3 years ago by
Istvan Albert
98k
70
votes
20
replies
81k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 4 months ago by
Ram
39k • written 12.6 years ago by
Unode
▴ 180
69
votes
25
replies
6.3k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 3 months ago by
Ram
39k • written 13.2 years ago by
Dave Gerrard
▴ 190
69
votes
39
replies
3.4k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
meta
biostars
updated 21 days ago by
Ram
39k • written 6.0 years ago by
John
13k
68
votes
22
replies
6.6k
views
16 follow
Forum:
Learning Python: list of resources
python
updated 7 weeks ago by
Ram
39k • written 6.6 years ago by
dago
★ 2.8k
68
votes
48
replies
7.1k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 21 days ago by
Ram
39k • written 5.9 years ago by
Istvan Albert
98k
1,000 results • Page
3 of 20
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data
by
Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
by
Vincent Laufer
★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column
by
atemedorri137798
• 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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