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854 results • Page 1 of 18
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328
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54
replies
61k
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45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 24 days ago by 41k • written 13.7 years ago by 24k
85
votes
49
replies
9.4k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 24 days ago by 41k • written 13.7 years ago by 3.4k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 29 days ago by 41k • written 10.1 years ago by ★ 7.8k
175
votes
46
replies
18k
views
26 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
12 days ago by Istvan Albert 99k
185
votes
43
replies
81k
views
29 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 24 days ago by 41k • written 13.7 years ago by ★ 1.6k
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 9 days ago by 22k • written 10.1 years ago by ★ 3.6k
172
votes
34
replies
25k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 24 days ago by 41k • written 13.7 years ago by 53k
118
votes
31
replies
191k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 18 days ago by 41k • written 13.6 years ago by 11k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 18 days ago by 41k • written 13.6 years ago by 18k
124
votes
29
replies
6.9k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 24 days ago by 41k • written 13.7 years ago by 7.4k
43
votes
28
replies
5.2k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 21 days ago by 41k • written 13.7 years ago by 11k
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 21 days ago by 41k • written 13.6 years ago by 4.5k
27
votes
27
replies
10.0k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 24 days ago by 41k • written 13.7 years ago by 53k
76
votes
26
replies
112k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 8 days ago by ★ 2.8k • written 8.6 years ago by ▴ 260
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 21 days ago by 41k • written 13.7 years ago by 158k
51
votes
25
replies
6.6k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 24 days ago by 41k • written 13.7 years ago by 53k
69
votes
25
replies
6.7k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 24 days ago by 41k • written 13.7 years ago by ▴ 190
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 18 days ago by 41k • written 13.6 years ago by 28k
61
votes
23
replies
54k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 10 days ago by ★ 1.2k • written 10.8 years ago by ★ 1.3k
15
votes
22
replies
8.3k
views
What Are The Most Reliable Normalization Methods For Microarrays?
microarray
updated 24 days ago by 41k • written 13.7 years ago by 3.4k
43
votes
21
replies
5.1k
views
9 follow
Helping Biostar Grow
biostars
updated 21 days ago by 41k • written 13.7 years ago by 11k
48
votes
21
replies
4.8k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 18 days ago by 41k • written 13.6 years ago by 4.9k
23
votes
21
replies
7.7k
views
9 follow
fastest UMAP method
UMAP R
updated 16 days ago by ★ 25k • written 4.1 years ago by ▴ 30
78
votes
21
replies
35k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 15 days ago by • 0 • written 9.6 years ago by ▴ 650
22
votes
21
replies
4.4k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 18 days ago by 41k • written 13.6 years ago by 18k
10
votes
21
replies
5.7k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R lumi LIMMA
updated 27 days ago by ★ 6.5k • written 3.7 years ago by ▴ 50
18
votes
20
replies
3.9k
views
9 follow
Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
project education
updated 24 days ago by 41k • written 13.7 years ago by ▴ 70
37
votes
20
replies
6.8k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 18 days ago by 41k • written 13.6 years ago by 11k
15
votes
20
replies
1.1k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
7 days ago by Axzd ▴ 50
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 24 days ago by 41k • written 13.7 years ago by ▴ 270
46
votes
18
replies
9.5k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 24 days ago by 41k • written 13.7 years ago by 3.4k
48
votes
18
replies
31k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 18 days ago by 41k • written 13.6 years ago by ★ 1.6k
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 24 days ago by 41k • written 13.7 years ago by 18k
39
votes
18
replies
5.7k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 18 days ago by 41k • written 13.6 years ago by ▴ 380
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 24 days ago by 41k • written 13.7 years ago by ▴ 390
36
votes
17
replies
3.4k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 24 days ago by 41k • written 13.7 years ago by 28k
15
votes
16
replies
4.6k
views
Gene Expression Experiment Using Ngs Data
next-gen-sequencing gene-expression
updated 18 days ago by 41k • written 13.6 years ago by 11k
26
votes
16
replies
6.3k
views
Which Human Tumor Cell Line/Sample Genomes Have Been Already Sequenced Completely?
genome next-gen-sequencing
updated 24 days ago by 41k • written 13.7 years ago by 4.3k
9
votes
15
replies
834
views
STAR output
STAR
updated 14 days ago by 41k • written 14 days ago by • 0
9
votes
15
replies
784
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
3 days ago by analyst ▴ 10
74
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 18 days ago by 41k • written 13.6 years ago by 158k
39
votes
15
replies
22k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 24 days ago by 41k • written 13.7 years ago by ▴ 790
12
votes
15
replies
4.3k
views
8 follow
for go enrichment analysis which tool do you recommend?
RNA-Seq go
updated 29 days ago by 3.1k • written 3.2 years ago by ▴ 40
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 18 days ago by 158k • written 13.6 years ago by ▴ 660
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 24 days ago by 41k • written 13.7 years ago by ▴ 270
20
votes
14
replies
4.7k
views
6 follow
Hardware Resources For Hpc In Bioinformatics
hpc
updated 24 days ago by 41k • written 13.7 years ago by 3.4k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 25 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
2
votes
14
replies
954
views
How to slice a CRAM file into the 50kb regions padded with 1kb?
GATK BED CRAM WGS
updated 21 days ago by 78k • written 25 days ago by • 0
17
votes
14
replies
13k
views
10 follow
Converting Ab1 Trace Files Into Scf Trace Files
sequence
updated 21 days ago by 41k • written 13.7 years ago by 4.5k
28
votes
14
replies
10k
views
7 follow
Compare Two Protein Sequences Using Local Blast
biopython blast
updated 24 days ago by 41k • written 13.7 years ago by ▴ 120
854 results • Page 1 of 18
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Recent Awards • All
Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
Popular Question to Gama313 ▴ 120
Popular Question to nanodano ▴ 30
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Scholar to jared.andrews07 ★ 16k
Recent Replies
Comment: "MethylKit" package for WGBS data by viveksomya123 • 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat? by synat.keam ▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization by geneontologyhelp ▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
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