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855 results • Page 1 of 18
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328
votes
54
replies
61k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 29 days ago by 41k • written 13.7 years ago by 24k
185
votes
43
replies
81k
views
29 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 29 days ago by 41k • written 13.7 years ago by ★ 1.6k
175
votes
46
replies
18k
views
26 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
17 days ago by Istvan Albert 99k
172
votes
34
replies
25k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 29 days ago by 41k • written 13.7 years ago by 53k
142
votes
14
replies
167k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 26 days ago by 41k • written 13.7 years ago by 158k
124
votes
29
replies
6.9k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 29 days ago by 41k • written 13.7 years ago by 7.4k
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
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
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
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
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
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 23 days ago by 41k • written 13.6 years ago by 28k
78
votes
21
replies
35k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 20 days ago by • 0 • written 9.6 years ago by ▴ 650
76
votes
26
replies
112k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 13 days ago by ★ 2.8k • written 8.6 years ago by ▴ 260
74
votes
32
replies
4.9k
views
12 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 2 days ago by 41k • written 6 months ago by ▴ 770
74
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 23 days ago by 41k • written 13.6 years ago by 158k
72
votes
27
replies
27k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 days ago by • 0 • written 9.8 years ago by 99k
69
votes
25
replies
6.8k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 29 days ago by 41k • written 13.7 years ago by ▴ 190
61
votes
23
replies
54k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 15 days ago by ★ 1.2k • written 10.8 years ago by ★ 1.3k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 23 days ago by 41k • written 13.7 years ago by 18k
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
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
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
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
48
votes
18
replies
31k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 23 days ago by 41k • written 13.6 years ago by ★ 1.6k
48
votes
21
replies
4.8k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 23 days ago by 41k • written 13.6 years ago by 4.9k
46
votes
18
replies
9.5k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 29 days ago by 41k • written 13.7 years ago by 3.4k
43
votes
28
replies
5.2k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 26 days ago by 41k • written 13.7 years ago by 11k
43
votes
21
replies
5.1k
views
9 follow
Helping Biostar Grow
biostars
updated 26 days ago by 41k • written 13.7 years ago by 11k
40
votes
19
replies
9.3k
views
12 follow
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers conference
updated 29 days ago by 41k • written 13.7 years ago by ▴ 270
39
votes
18
replies
5.7k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 23 days ago by 41k • written 13.6 years ago by ▴ 380
39
votes
15
replies
22k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 29 days ago by 41k • written 13.7 years ago by ▴ 790
38
votes
14
replies
8.8k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl python biopython genome
updated 29 days ago by 41k • written 13.7 years ago by ▴ 270
37
votes
20
replies
6.8k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 23 days ago by 41k • written 13.7 years ago by 11k
36
votes
17
replies
3.4k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 29 days ago by 41k • written 13.7 years ago by 28k
35
votes
10
replies
15k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq peak-calling
updated 23 days ago by 41k • written 13.7 years ago by ★ 1.4k
33
votes
9
replies
9.9k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing fastq c
updated 29 days ago by 41k • written 13.7 years ago by 22k
32
votes
4
replies
9.2k
views
Fastq Qualities For Solexa/Illumina
sequencing-quality next-gen-sequencing fastq
updated 26 days ago by 41k • written 13.7 years ago by 158k
31
votes
11
replies
5.5k
views
6 follow
Assessing Cluster Reliability/Stability In Microarray Experiments
clustering microarray gene
updated 26 days ago by 41k • written 13.7 years ago by ★ 2.2k
31
votes
8
replies
12k
views
Experiences With Clc Genomics Workbench (Or Other Commercial Tools) For Next-Gen Sequencing
next-gen-sequencing
updated 23 days ago by 41k • written 13.6 years ago by 99k
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray annotation affymetrix probeset
updated 29 days ago by 41k • written 13.7 years ago by 18k
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books online
updated 23 days ago by 41k • written 13.6 years ago by ★ 1.0k
28
votes
14
replies
10k
views
7 follow
Compare Two Protein Sequences Using Local Blast
biopython blast
updated 29 days ago by 41k • written 13.7 years ago by ▴ 120
28
votes
27
replies
14k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython python fastq next-gen-sequencing
updated 26 days ago by 41k • written 13.7 years ago by 4.5k
28
votes
13
replies
14k
views
7 follow
Create Consensus Sequences For Sequence Pairs Within A Multiple Alignment?
consensus phylogenetics fasta multiple-alignment
updated 26 days ago by 41k • written 13.7 years ago by ★ 2.0k
27
votes
10
replies
4.2k
views
7 follow
Which Are All The Databases For Annotations Of Biological Pathways?
pathway database annotation
updated 26 days ago by 41k • written 13.7 years ago by 28k
27
votes
4
replies
2.5k
views
How Should A Departing Programmer Organize Things For Successors?
software
updated 23 days ago by 41k • written 13.6 years ago by ▴ 330
27
votes
27
replies
10.0k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 29 days ago by 41k • written 13.7 years ago by 53k
26
votes
16
replies
6.3k
views
Which Human Tumor Cell Line/Sample Genomes Have Been Already Sequenced Completely?
genome next-gen-sequencing
updated 29 days ago by 41k • written 13.7 years ago by 4.3k
26
votes
11
replies
4.8k
views
7 follow
How To Filter Affymetrix Probes Related To Murine Genes Encoding Membran Proteins
affymetrix gene annotation mouse gene
updated 29 days ago by 41k • written 13.7 years ago by 4.3k
855 results • Page 1 of 18
Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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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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