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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 mapping in regions whe…
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…
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…
Comment: ScRNA data question
by
starswillfade
▴
10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴
10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to?
The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically:
If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later.
library(GenomicFeatures)
library(rtracklayer)
## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★
5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
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