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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
121
votes
54
replies
94k
views
23 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 weeks ago by
William
▴ 20 • written 9.3 years ago by
kay
▴ 340
121
votes
35
replies
40k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 4 months ago by
Ram
40k • written 6.3 years ago by
ropolocan
▴ 790
120
votes
33
replies
37k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 4 months ago by
carlopecoraro2
★ 2.3k • written 10.1 years ago by
Eric Normandeau
11k
118
votes
26
replies
34k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 6 months ago by
e.r.zakiev
▴ 80 • written 8.3 years ago by
mhockin
▴ 610
118
votes
74
replies
43k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 10 months ago by
GenoMax
134k • written 12.8 years ago by
Casbon
★ 3.3k
117
votes
59
replies
31k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 7 months ago by
Ram
40k • written 8.4 years ago by
Angelo Victoria
▴ 30
116
votes
66
replies
43k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 6 months ago by
Ram
40k • written 5.2 years ago by
ATpoint
76k
116
votes
35
replies
7.5k
views
18 follow
Forum:
Is Biostar Killing The Bioinformatics Core?
core
biostars
updated 7 months ago by
Ram
40k • written 10.5 years ago by
Jeremy Leipzig
21k
115
votes
25
replies
67k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 7 months ago by
Miguel
▴ 10 • written 12.6 years ago by
Pierre Lindenbaum
157k
113
votes
53
replies
5.8k
views
16 follow
Forum:
Middle author, but not first author projects. How would you approach this?
authorship
career-development
updated 3 months ago by
Ram
40k • written 4.5 years ago by
pet.bioinformatician
▴ 170
110
votes
37
replies
7.4k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 7 months ago by
Ram
40k • written 12.0 years ago by
Pierre Lindenbaum
157k
106
votes
23
replies
21k
views
16 follow
Forum:
How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 6 months ago by
Ram
40k • written 9.6 years ago by
epigene
▴ 590
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 3 days ago by
zx8754
11k • written 10.7 years ago by
henryvuong
▴ 810
105
votes
46
replies
12k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 6 months ago by
Ram
40k • written 10.1 years ago by
ugly.betty77
★ 1.1k
104
votes
12
replies
75k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 11 months ago by
Ram
40k • written 11.9 years ago by
Bioscientist
★ 1.7k
104
votes
6
replies
24k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 6 months ago by
Ram
40k • written 5.1 years ago by
finswimmer
16k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 7 months ago by
Ram
40k • written 11.3 years ago by
Anjan
▴ 830
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 3 months ago by
Ram
40k • written 13.5 years ago by
Biostar User
★ 1.0k
102
votes
44
replies
8.3k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 6 months ago by
Ram
40k • written 10.1 years ago by
brentp
24k
100
votes
15
replies
104k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 6 months ago by
Genetics
▴ 20 • written 11.3 years ago by
GouthamAtla
12k
100
votes
38
replies
28k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 22 days ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
99
votes
8
replies
28k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 5 months ago by
Ram
40k • written 7.6 years ago by
Jordan Anaya
★ 1.1k
99
votes
16
replies
31k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 6 months ago by
Ram
40k • written 7.1 years ago by
Jean-Karim Heriche
26k
99
votes
32
replies
105k
views
21 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 6 weeks ago by
ammar.husami
• 0 • written 11.3 years ago by
GPR
▴ 390
99
votes
21
replies
8.3k
views
14 follow
Forum:
How Has Bioinformatics Improved Over Time?
bioinformatics
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Kate
▴ 370
98
votes
41
replies
5.0k
views
17 follow
Forum:
I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error
next-gen-sequencing
updated 5 months ago by
Ram
40k • written 7.1 years ago by
moxu
▴ 510
97
votes
27
replies
81k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 4 months ago by
NIRJHAR
• 0 • written 11.3 years ago by
Rubal7
▴ 820
95
votes
25
replies
32k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 7 months ago by
Ram
40k • written 11.0 years ago by
Istvan Albert
98k
93
votes
105
replies
39k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 6 months ago by
Ram
40k • written 5.1 years ago by
Kevin Blighe
86k
93
votes
19
replies
57k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 3 months ago by
Ram
40k • written 13.0 years ago by
Niek De Klein
★ 2.6k
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by
Dan
▴ 140 • written 11.2 years ago by
abi
▴ 380
93
votes
50
replies
15k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 6 months ago by
Ram
40k • written 9.8 years ago by
Istvan Albert
98k
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 7 months ago by
Ram
40k • written 12.2 years ago by
Andra Waagmeester
3.2k
92
votes
18
replies
63k
views
12 follow
Sequence length from Fasta
fasta
updated 9 months ago by
Ram
40k • written 8.9 years ago by
bongbang
▴ 80
91
votes
20
replies
19k
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 11 months ago by
Ram
40k • written 9.3 years ago by
Obi Griffith
20k
90
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 6 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
90
votes
16
replies
21k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat
batch-effect
sva
updated 7 months ago by
madbadradscientist
▴ 20 • written 8.3 years ago by
Christian
★ 3.0k
88
votes
24
replies
5.1k
views
10 follow
Forum:
How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 7 months ago by
Ram
40k • written 10.6 years ago by
aidan-budd
1.9k
87
votes
13
replies
20k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career
general
updated 7 months ago by
Ram
40k • written 13.5 years ago by
Yuri
★ 1.6k
86
votes
29
replies
9.1k
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 5 months ago by
Ram
40k • written 7.3 years ago by
Michael
53k
86
votes
22
replies
80k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 10 weeks ago by
sifa.khan
• 0 • written 5.2 years ago by
otwtgin2010
▴ 580
85
votes
16
replies
89k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 10 months ago by
bhanu.chandra1
▴ 50 • written 8.4 years ago by
Prakki Rama
★ 2.7k
85
votes
2
replies
56k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 6 months ago by
Ram
40k • written 10.2 years ago by
Eric Normandeau
11k
84
votes
21
replies
18k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 months ago by
Ram
40k • written 2.9 years ago by
Hamid Ghaedi
3.0k
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 weeks ago by
amziepickles
• 0 • written 7.5 years ago by
Obi Griffith
20k
84
votes
22
replies
4.0k
views
12 follow
Forum:
is fortran still used in bioinformatics?
FORTRAN
R
updated 6 months ago by
Ram
40k • written 4.3 years ago by
Manoj
▴ 180
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 3 months ago by
adelheidkratzer
• 0 • written 5.3 years ago by
egeulgen
★ 1.3k
83
votes
20
replies
18k
views
17 follow
How Do Pathway Databases Compare?
pathway
database
subjective
updated 8 weeks ago by
Peter Karp
▴ 30 • written 12.9 years ago by
Shigeta
▴ 470
82
votes
32
replies
7.0k
views
13 follow
Forum:
Shall We Go Back To Stackexchange?
meta
updated 7 months ago by
Ram
40k • written 10.8 years ago by
14134125465346445
★ 3.6k
82
votes
19
replies
12k
views
8 follow
Future Directions In Bioinformatics
subjective
career
updated 7 months ago by
Ram
40k • written 12.8 years ago by
Hranjeev
★ 1.5k
1,000 results • Page
2 of 20
Recent Votes
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Salmon index not progressing
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Salmon index not progressing
Answer: Filtering VCF to divide with equal sizes
Answer: Filtering VCF to divide with equal sizes
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Recent Replies
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★ 2.5k
you expect to have aneuploidy only in the knockout?
Comment: STAR index not working
by
camillab.
▴ 130
thank you! I am following GenoMax suggestion and I am trying with `salmon` but it is stuck as well. it's not making any progress.....
Comment: Scanning for ultra-hot topics in science via pubmed, or using other tools
by
LauferVA
3.7k
@genomax , thank you. this is a really great start. i will likely use a python based approach, but other than that, i think ill proceed e…
Comment: OMA in AWS cloud
by
Ram
40k
> if it is possible. Yes, most things are possible on AWS. > I didn't find anything in the web. I *highly* **highly** doubt that.
Comment: genome data downloads for various strains
by
Ram
40k
Is there a reason you keep replying to your own messages instead of writing one complete comment and leaving it at that?
Comment: How to download genomes and proteins from JGI in bulk via the command line?
by
GenoMax
134k
You probably know about https://github.com/glarue/jgi-query already? It is not going to be as simple to download from JGI compared to NCB…
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