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19,757 results • Page 2 of 396
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122
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44
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10k
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24 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 5 weeks ago by 41k • written 11.0 years ago by 99k
121
votes
35
replies
41k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 6 months ago by 41k • written 6.5 years ago by ▴ 810
121
votes
44
replies
20k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 9 months ago by 41k • written 13.5 years ago by 5.3k
121
votes
56
replies
97k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 9 weeks ago by ▴ 20 • written 9.5 years ago by ▴ 340
120
votes
33
replies
38k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 7 months ago by ★ 2.4k • written 10.3 years ago by 11k
118
votes
31
replies
191k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 23 days ago by 41k • written 13.7 years ago by 11k
118
votes
26
replies
35k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 9 months ago by ▴ 170 • written 8.6 years ago by ▴ 610
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
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 10 months ago by 41k • written 8.6 years ago by ▴ 30
116
votes
25
replies
68k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 10 months ago by ▴ 20 • written 12.9 years ago by 158k
116
votes
35
replies
7.8k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 9 months ago by 41k • written 10.7 years ago by 22k
113
votes
53
replies
6.3k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 6 months ago by 41k • written 4.7 years ago by ▴ 170
110
votes
37
replies
7.8k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 9 months ago by 41k • written 12.2 years ago by 158k
106
votes
23
replies
21k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 9 months ago by 41k • written 9.8 years ago by ▴ 590
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 9 months ago by 41k • written 10.3 years ago by ★ 1.1k
105
votes
26
replies
41k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 11 weeks ago by 11k • written 10.9 years ago by ▴ 810
104
votes
6
replies
25k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.3 years ago by 16k
102
votes
19
replies
18k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 9 months ago by 41k • written 11.5 years ago by ▴ 830
102
votes
44
replies
8.6k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 9 months ago by 41k • written 10.3 years ago by 24k
102
votes
30
replies
61k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 6 weeks ago by 41k • written 13.8 years ago by ★ 1.0k
101
votes
34
replies
108k
views
23 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 9 weeks ago by 14k • written 11.5 years ago by ▴ 390
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 14 days ago by 22k • written 10.1 years ago by ★ 3.6k
100
votes
15
replies
107k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 9 months ago by ▴ 20 • written 11.5 years ago by 12k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 months ago by 41k • written 7.8 years ago by ★ 1.1k
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
99
votes
21
replies
8.6k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 9 months ago by 41k • written 10.9 years ago by ▴ 370
98
votes
41
replies
5.4k
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 8 months ago by 41k • written 7.3 years ago by ▴ 510
98
votes
27
replies
84k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 6 months ago by • 0 • written 11.5 years ago by ▴ 830
97
votes
19
replies
92k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 7 weeks ago by 41k • written 13.8 years ago by 28k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 26 days ago by 41k • written 13.7 years ago by 158k
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.3 years ago by 86k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 9 months ago by 41k • written 11.2 years ago by 99k
95
votes
39
replies
147k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 7 months ago by ▴ 160 • written 11.4 years ago by ▴ 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 9 months ago by 41k • written 10.0 years ago by 99k
93
votes
19
replies
58k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 5 months ago by 41k • written 13.2 years ago by ★ 2.6k
93
votes
16
replies
22k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 10 months ago by ▴ 20 • written 8.5 years ago by ★ 3.0k
93
votes
18
replies
66k
views
12 follow
Sequence length from Fasta
fasta
updated 11 months ago by 41k • written 9.1 years ago by ▴ 80
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 9 months ago by 41k • written 12.4 years ago by 3.2k
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 9 months ago by 41k • written 10.1 years ago by 20k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 weeks ago by 41k • written 10.1 years ago by ★ 7.8k
89
votes
12
replies
20k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 29 days ago by 41k • written 13.7 years ago by ★ 1.6k
88
votes
22
replies
84k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.4 years ago by ▴ 580
88
votes
24
replies
5.3k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 9 months ago by 41k • written 10.8 years ago by 1.9k
86
votes
29
replies
9.4k
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 months ago by 41k • written 7.5 years ago by 53k
85
votes
49
replies
9.5k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 29 days ago by 41k • written 13.7 years ago by 3.4k
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 9 months ago by 41k • written 3.1 years ago by 3.1k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
84
votes
22
replies
4.2k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 9 months ago by 41k • written 4.5 years ago by ▴ 180
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.5 years ago by ★ 1.3k
19,757 results • Page 2 of 396
Recent Votes
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
A: Extract somatic mutations and germline mutations from variant calling files?
C: visualizing mutational data using Maftools for reference genome hg19
Answer: Ambient RNA removal method that generates whole (integer) counts
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Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
Scholar to jared.andrews07 ★ 16k
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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