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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
95
votes
6
replies
37k
views
In Sam Format, Clarify The Meaning Of The "0" Flag.
sam
updated 13.1 years ago by
Jts
★ 1.4k • written 13.1 years ago by
tflutre
▴ 580
95
votes
5
replies
55k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools
clipped-reads
soft-clip
bam
hard-clip
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
94
votes
31
replies
39k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python
alignment
next-gen
sequencing
database
updated 2.1 years ago by
Ram
43k • written 13.7 years ago by
User 1586
▴ 280
94
votes
16
replies
23k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat
batch-effect
sva
updated 15 months ago by
madbadradscientist
▴ 20 • written 8.9 years ago by
Christian
★ 3.0k
93
votes
19
replies
59k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 10 months ago by
Ram
43k • written 13.6 years ago by
Niek De Klein
★ 2.6k
93
votes
23
replies
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
93
votes
32
replies
33k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 12.2 years ago by
Sat3Lite
▴ 150
93
votes
18
replies
70k
views
12 follow
Sequence length from Fasta
fasta
updated 16 months ago by
Ram
43k • written 9.5 years ago by
bongbang
▴ 80
93
votes
50
replies
16k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Istvan Albert
100k
92
votes
20
replies
28k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r
visualization
updated 23 months ago by
Ram
43k • written 12.2 years ago by
John
★ 1.5k
92
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.4 years ago by
BioNovice247
▴ 20 • written 6.5 years ago by
rachel.kubik12
▴ 220
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 14 months ago by
Ram
43k • written 12.8 years ago by
Andra Waagmeester
3.2k
91
votes
20
replies
20k
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 18 months ago by
Ram
43k • written 9.9 years ago by
Obi Griffith
20k
91
votes
21
replies
53k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq
read
updated 10.4 years ago by
earonesty
▴ 250 • written 11.5 years ago by
siddharth.sethi5
▴ 270
91
votes
10
replies
108k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 12.0 years ago by
Guangchuang Yu
★ 2.6k • written 12.0 years ago by
Wayne
★ 1.0k
91
votes
25
replies
62k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks
selection
software
updated 19 months ago by
Michael
54k • written 13.2 years ago by
Jarretinha
3.4k
90
votes
26
replies
38k
views
22 follow
Extracting Sequence From A 3Gb Fasta File
sequence
retrieval
fasta
perl
updated 6.2 years ago by
andplaia
• 0 • written 13.9 years ago by
Divya
▴ 260
90
votes
19
replies
32k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 13 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 24 months ago by
Ram
43k • written 13.0 years ago by
Ryan D
★ 3.4k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
89
votes
31
replies
14k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs
visualization
genomics
updated 21 months ago by
Ram
43k • written 12.1 years ago by
John
★ 1.5k
89
votes
12
replies
21k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Yuri
★ 1.7k
88
votes
24
replies
9.7k
views
14 follow
Project Euler Equivalent For Bioinformatics?
online
updated 7.2 years ago by
Biostar
20 • written 13.8 years ago by
Gabriel Mitchell
▴ 520
88
votes
32
replies
9.5k
views
11 follow
Forum:
Vintage / unconventional pictures for Bioinformatics
history
picture
updated 2.1 years ago by
Ram
43k • written 9.5 years ago by
Pierre Lindenbaum
161k
88
votes
36
replies
40k
views
15 follow
1000 Genomes Ld Calculation
genome
linkage
gwas
updated 10.2 years ago by
Leandro Lima
▴ 970 • written 13.5 years ago by
Ryan D
★ 3.4k
88
votes
24
replies
5.6k
views
10 follow
Forum:
How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 14 months ago by
Ram
43k • written 11.2 years ago by
aidan-budd
1.9k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
87
votes
12
replies
56k
views
9 follow
What are chimeric reads?
sequence
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
zhangz.cs
▴ 300
87
votes
37
replies
52k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 2.1 years ago by
Ram
43k • written 10.8 years ago by
Hunter
▴ 110
87
votes
2
replies
59k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by
Ram
43k • written 10.8 years ago by
Eric Normandeau
11k
87
votes
25
replies
52k
views
21 follow
How To Split A Multiple Fasta
fasta
split
updated 2.3 years ago by
Ram
43k • written 13.7 years ago by
Gvj
▴ 470
87
votes
11
replies
19k
views
8 follow
Good Gwas Papers / Resources
gwas
literature
snp
updated 13.7 years ago by
Larry_Parnell
16k • written 13.7 years ago by
brentp
24k
86
votes
29
replies
9.9k
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 12 months ago by
Ram
43k • written 7.9 years ago by
Michael
54k
85
votes
16
replies
97k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 17 months ago by
bhanu.chandra1
▴ 50 • written 9.0 years ago by
Prakki Rama
★ 2.7k
85
votes
19
replies
44k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly
quality
next-gen
updated 2.2 years ago by
WANG
▴ 10 • written 11.3 years ago by
diltsjeri
▴ 470
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
84
votes
22
replies
4.6k
views
12 follow
Forum:
is fortran still used in bioinformatics?
FORTRAN
R
updated 13 months ago by
Ram
43k • written 4.8 years ago by
Manoj
▴ 190
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
84
votes
36
replies
19k
views
13 follow
Forum:
Benchmark - Comparison of Different NGS Mappers
mRNA-Seq
benchmark
NGS-mapper
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
David Langenberger
11k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway
database
subjective
updated 9 months ago by
Peter Karp
▴ 30 • written 13.5 years ago by
Shigeta
▴ 470
83
votes
30
replies
6.7k
views
18 follow
Forum:
Optimal design for bioinformatics "lab" space?
design
lab-space
updated 22 months ago by
Ram
43k • written 9.0 years ago by
Casey Bergman
18k
83
votes
46
replies
8.7k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 5 weeks ago by
LauferVA
4.2k • written 10 months ago by
Sasha
▴ 840
82
votes
27
replies
54k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 8.0 years ago by
noirot.celine
▴ 50 • written 11.6 years ago by
thiago84naka
▴ 130
82
votes
13
replies
41k
views
7 follow
Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?
snp
snp
updated 3.7 years ago by
Biostar
20 • written 13.3 years ago by
Yahan
▴ 210
82
votes
19
replies
13k
views
8 follow
Future Directions In Bioinformatics
subjective
career
updated 14 months ago by
Ram
43k • written 13.4 years ago by
Hranjeev
★ 1.5k
82
votes
11
replies
30k
views
10 follow
Qiime Vs Mothur : Why Use One Over The Other?
metagenomics
updated 7.6 years ago by
shizhaojingszj
• 0 • written 10.1 years ago by
amcrisan
▴ 370
82
votes
32
replies
7.7k
views
13 follow
Forum:
Shall We Go Back To Stackexchange?
meta
updated 14 months ago by
Ram
43k • written 11.4 years ago by
14134125465346445
★ 3.6k
81
votes
8
replies
8.6k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 13 months ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
19k
81
votes
21
replies
5.0k
views
16 follow
Forum:
[UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Sinji
★ 3.2k
1,000 results • Page
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Comment: To get p-values for the TPM
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dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
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• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
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• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
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There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
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I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies
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kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
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100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
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There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
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Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
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