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16 results • Page
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11
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476
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
19 hours ago by
atowns21
• 0
0
votes
7
replies
271
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 4 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
1
vote
2
replies
217
views
PCA plot
DESeq2
PCAplot
updated 10 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
221
views
Annovar using R package
Annovar
gnomAD
R
23 hours ago by
DKA
▴ 40
0
votes
2
replies
170
views
Highest variable features in single cell data
single-cell
updated 23 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
118
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
0
votes
0
replies
78
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
10 hours ago by
HarperReed
• 0
0
votes
0
replies
38
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 3 hours ago by
Ram
43k • written 4 hours ago by
vanbelj
▴ 40
0
votes
0
replies
57
views
RNA-seq: full length gene
RNA-seq
updated 3 hours ago by
Ram
43k • written 13 hours ago by
Nargis
• 0
0
votes
0
replies
39
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
hagl
▴ 10
0
votes
0
replies
18
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 30 minutes ago by
Ram
43k • written 1 hour ago by
Guille
• 0
0
votes
0
replies
68
views
Designing single-stable RNA molecules
structure
RNA
22 hours ago by
Edna
• 0
0
votes
0
replies
80
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
22 hours ago by
simplitia
▴ 130
0
votes
0
replies
53
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
15 hours ago by
turcoa1
• 0
0
votes
0
replies
55
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
13 hours ago by
SineWave
• 0
1
vote
0
replies
55
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
13 hours ago by
KABILAN
▴ 50
16 results • Page
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Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
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