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1,000 results • Page 5 of 20
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56
votes
35
replies
13k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 8 weeks ago by 86k • written 5.8 years ago by ▴ 520
56
votes
8
replies
7.8k
views
8 follow
What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expr…
RNA-Seq rna-seq
updated 7 weeks ago by • 0 • written 5.7 years ago by ▴ 150
56
votes
12
replies
12k
views
9 follow
What Are The Public Sql Servers For Bioinformatics ?
online-server sql
updated 29 days ago by 41k • written 13.7 years ago by 158k
56
votes
23
replies
4.6k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 5 months ago by 41k • written 7.4 years ago by 14k
56
votes
19
replies
3.9k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 6 months ago by 41k • written 6.4 years ago by 23k
55
votes
13
replies
8.2k
views
7 follow
Rna-Seq Data Analysis & Good Review/Research Article On Same
RNA-seq
updated 9 months ago by 41k • written 12.7 years ago by ★ 2.8k
55
votes
23
replies
26k
views
11 follow
Remove duplicates in fasta file based on ID
fasta sort sed
updated 10 months ago by 41k • written 8.5 years ago by ▴ 210
54
votes
16
replies
5.4k
views
13 follow
Forum: The new era of bioinformatics: simple and fast tools, fewer and more informative data
kallisto computational-cost
updated 10 months ago by 41k • written 8.6 years ago by 99k
54
votes
10
replies
21k
views
10 follow
Finding Common Motifs In Sequences
motif
updated 7 weeks ago by 41k • written 14.2 years ago by ▴ 130
54
votes
17
replies
5.4k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer annotation
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
54
votes
7
replies
3.9k
views
6 follow
Tool: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 5 months ago by 41k • written 10.5 years ago by ▴ 40
54
votes
24
replies
3.9k
views
12 follow
News: Big news from Microsoft. BASH on windows.
windows
updated 8 months ago by 41k • written 7.7 years ago by ★ 3.2k
54
votes
34
replies
4.5k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 9 months ago by 41k • written 13.0 years ago by 99k
54
votes
52
replies
47k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 5 months ago by 41k • written 9.3 years ago by 7.5k
54
votes
13
replies
10k
views
6 follow
Tool: Bedtools: Analyzing Genomic Features
bedtools
updated 5 months ago by 41k • written 11.6 years ago by 99k
53
votes
19
replies
43k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 9 months ago by 41k • written 11.6 years ago by 11k
53
votes
27
replies
4.1k
views
11 follow
Should General Programming Questions Actually Be Posted To Biostar?
meta biostars
updated 9 months ago by 41k • written 12.4 years ago by ★ 1.6k
53
votes
13
replies
5.3k
views
6 follow
Tool: I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 11 months ago by 41k • written 8.5 years ago by ★ 3.9k
53
votes
31
replies
6.1k
views
15 follow
Biostar Flyer For Outreach
biostars
updated 9 months ago by 41k • written 13.1 years ago by 11k
53
votes
13
replies
7.6k
views
9 follow
Has Enhancer And Transcription Factor Binding Site Prediction Already Been Made Redundant?
transcription-factor-binding-site
updated 6 weeks ago by 41k • written 13.8 years ago by ★ 1.3k
53
votes
11
replies
27k
views
10 follow
Out Of Disk Space With Picard Tools ?
picard
updated 5 months ago by 41k • written 11.7 years ago by ★ 2.9k
52
votes
8
replies
4.6k
views
8 follow
Forum: What Is The Proper Way To Think About Reinventing The Wheel As A Bioinformatician?
software-development
updated 9 months ago by 41k • written 10.8 years ago by ★ 4.1k
52
votes
8
replies
20k
views
6 follow
Fast Interval Intersection Methodologies
genomics
updated 7 weeks ago by 41k • written 13.8 years ago by ★ 1.0k
52
votes
18
replies
6.1k
views
14 follow
Forum: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
meta biostars
updated 9 months ago by 41k • written 10.2 years ago by ★ 1.1k
52
votes
11
replies
36k
views
8 follow
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
RNA-Seq
updated 10 months ago by 41k • written 9.4 years ago by ▴ 210
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 23 days ago by 158k • written 13.6 years ago by ▴ 660
52
votes
21
replies
48k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 5 months ago by 41k • written 11.7 years ago by ★ 1.5k
51
votes
16
replies
5.5k
views
11 follow
Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2011?
papers
updated 10 months ago by 41k • written 12.0 years ago by ★ 2.9k
51
votes
14
replies
80k
views
10 follow
Tutorial: Using R in Conda
R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 780
51
votes
25
replies
6.6k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 29 days ago by 41k • written 13.7 years ago by 53k
51
votes
17
replies
3.7k
views
News: Biostars 3.0 is now under testing. It has groups, charms and other interesting features.
meta biostars
updated 9 months ago by 41k • written 8.7 years ago by 99k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 9 months ago by 41k • written 10.9 years ago by ▴ 300
51
votes
6
replies
17k
views
Decoy In Reference Assembly
1000genomes
updated 6 months ago by • 0 • written 10.5 years ago by ▴ 420
51
votes
15
replies
66k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts sequence fastq
updated 9 months ago by 41k • written 12.5 years ago by ★ 1.7k
51
votes
10
replies
2.9k
views
6 follow
Is Biostar A Research Advice Tool Or A Tutor (Helping Students) Or Both?
meta biostars homework
updated 9 months ago by 41k • written 12.8 years ago by 16k
50
votes
20
replies
5.6k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 9 months ago by 41k • written 7.8 years ago by ★ 1.1k
50
votes
10
replies
21k
views
9 follow
How Important Is Bioinformatics And How To Make A Case For It?
subjective education
updated 9 months ago by 41k • written 12.5 years ago by ★ 1.3k
50
votes
8
replies
9.3k
views
6 follow
Forum: Encode Commentary From Dan Graur
encode
updated 9 months ago by 41k • written 10.8 years ago by 16k
50
votes
23
replies
22k
views
13 follow
intersect VCF files
VCF
updated 10 months ago by 41k • written 7.8 years ago by ★ 1.4k
50
votes
3
replies
4.5k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
50
votes
19
replies
4.7k
views
7 follow
Forum: Proposal: Biostar Wants To Run Your Ads. Feedback Requested.
biostars
updated 9 months ago by 41k • written 10.8 years ago by 99k
50
votes
15
replies
29k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 4 months ago by ★ 3.3k • written 10.4 years ago by ▴ 940
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 9 months ago by 41k • written 3.2 years ago by 78k
50
votes
16
replies
13k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 5 months ago by 41k • written 10.2 years ago by ▴ 450
50
votes
18
replies
35k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 5 months ago by 41k • written 7.3 years ago by 13k
50
votes
4
replies
8.8k
views
Forum: How to add images to a Biostars post
how-to
10 months ago by Ram 41k
49
votes
36
replies
8.2k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 9 months ago by 41k • written 9.6 years ago by ▴ 110
49
votes
27
replies
6.7k
views
10 follow
Forum: Possible augmented reality tools for bioinformatics and current problems
visualization 3D augmented-reality
updated 8 months ago by 41k • written 8.1 years ago by ▴ 90
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 29 days ago by 41k • written 13.7 years ago by ▴ 390
49
votes
19
replies
7.0k
views
13 follow
Forum: Why Are There No Proteomics Questions In Biostar?
proteomics biostars
updated 9 months ago by 41k • written 13.1 years ago by ▴ 410
1,000 results • Page 5 of 20
Recent Votes
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
Answer: Ambient RNA removal method that generates whole (integer) counts
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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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