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9 results • Page
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Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 29 days ago by
Ram
41k • written 10.1 years ago by
Irsan
★ 7.8k
36
votes
14
replies
32k
views
14 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 25 days ago by
psschlogl
▴ 50 • written 3.3 years ago by
lavinia.gordon
▴ 160
19
votes
13
replies
7.9k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 29 days ago by
jude
• 0 • written 17 months ago by
ATpoint
78k
0
votes
4
replies
451
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
21 days ago by
Coremine Medical
▴ 20
5
votes
1
reply
4.3k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
6 hours ago by
GenoMax
136k
1
vote
0
replies
593
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 25 days ago by
Ram
41k • written 8 months ago by
Milad
▴ 10
2
votes
0
replies
941
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 18 days ago by
Ali
• 0 • written 10 months ago by
firestar
★ 1.6k
0
votes
0
replies
174
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
6 days ago by
rohitsatyam102
▴ 780
0
votes
0
replies
247
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
27 days ago by
rohitsatyam102
▴ 780
9 results • Page
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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 Replies
Answer: "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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