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6 results • Page
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Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 1 day ago by
Ram
40k • written 10.0 years ago by
Irsan
★ 7.7k
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 20 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 years ago by
Luke Crichton
▴ 410
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 6 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
4
votes
2
replies
2.3k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 23 days ago by
GenoMax
134k • written 3.4 years ago by
ATpoint
77k
1
vote
0
replies
177
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 15 days ago by
Ram
40k • written 15 days ago by
Pierre Lindenbaum
157k
0
votes
1
reply
184
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 16 days ago by
ATpoint
77k • written 16 days ago by
JC
▴ 30
6 results • Page
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Recent Votes
Comment: Frustrated with DEA results
Pedigree - Haplotype building and VCF files
A: Pedigree - Haplotype building and VCF files
A: Individual VCF files from main VCF file
Individual VCF files from main VCF file
A: Splitting vcf files to individual samples
Splitting vcf files to individual samples
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Recent Replies
Answer: Recommendations for extending contigs from denovo assembly to identify SV insert
by
shelkmike
▴ 980
Some time ago I made a tool Elloreas (https://github.com/shelkmike/Elloreas) that iteratively extends a contig using long reads. It can be …
Answer: How to get the gft file to run velocyto for velocity analysis?
by
ATpoint
77k
You need the same GTF file that was used during mapping of your 10x data. If you used CellRanger and it was mouse (given you used recent Ce…
Answer: Lower alignment rate when using collapsed reads
by
LChart
3.4k
Sequences are collapsed if they're sufficiently identical. Garbage (random) reads won't collapse. If you collapse the "good" reads and don'…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
(1) Yes; but you can simply subset the DESeq via `dds[,dds$donor != UNWANTED_DONOR]` (3) Given the initial results (and the MDS) that dono…
Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Sounds good! I just added a solution here.
Answer: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Running kallisto bus with the -n option will record the read numbers of the reads that have been successfully mapped in the output BUS file…
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
cfos4698
▴ 830
Just a comment re: your bash example reading from a file. Have you tried `while` instead of 'with'? ``` while read sample; do bcftools…
Comment: Split plink files by a number of SNPs
by
Raygozak
★ 1.4k
Out of curiosity, why would someone ask how to do something if they already knew how to do it or which tools to use? Also, the OP is not a…
Comment: Comparing multiple RNASeq studies
by
Zhenyu Zhang
▴ 980
no. The best you can do is to draw conclusion using one dataset, and validate your conclusion using other datasets.
Comment: comparision of umap single cell
by
synat.keam
▴ 80
Thank, Seniors.. I figured out the issue of my integration as I did not state the ``` reduction= "harmony" ```
Comment: Issue with merging in plink and eigensoft.
by
bk11
★ 1.2k
> I merged two datasets in plink1.9. It worked, but I did get the error > "multiple positions seen for variant" and "variants have the same…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
• 0
It worked now, after re-mapping with short-headed FASTA! :) Thanks a lot again for your time.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
svlachavas
▴ 780
Dear LChart, thanks a million for your detailed response and explanations !! Some quick updated comments (hopefully not disturb you furth…
Comment: Clustering in single cell
by
Chris
▴ 200
Just because the articles and tutorials I read, they usually clearly separate which I worry I did something wrong.
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
134k
> do you think the one or other option (using fasta with shortened > headers vs. bbmap.sh with trd=t option) would have other advantages or…
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