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Recent Replies
Comment: Sudden drop in coverage in single-cell RNA-sequencing data
by
tien
▴
10
Hi, sorry for my bad question. This screenshot is not about my data but my data behaves the same and I did take umi into account when plott…
Comment: How to calculate position-specific fastq stats?
by
O.rka
▴
610
Thanks, that's good to know. I ended up writing one last night and updated the question.
Comment: Are upset plots bad for differential expression analysis?
by
paulimer
▴
10
> Whichever direction has the smallest product of p-values (i.e., which is more significant under a Fisher's method meta-analysis)?
That's…
Answer: Filtering multiple-samples VCF by genotype with GATK
by
LChart
▴
380
I think you either need to escape the inner quotes, or use single outer-quotes and double inner quotes
`'vc.getGenotype("sample1").isHom…
Answer: RNAseq matrix input for WGCNA analysis
by
LChart
▴
380
You should be able to pass in `$abundance` to WGCNA methods directly:
```
library(tximportData)
library(tximport)
library(WGCNA)
d…
Comment: How to check Burrows-Wheeler Aligner (BWA) version on my terminal?
by
appropiate
▴
30
That was embarrassingly simple, thanks!
Answer: How to get intersected variants between multiple vcf files?
by
Jeremy Leipzig
20k
i would use vt to normalize and decompose your vcfs first - that should put all the multiallelic events on different lines
https://genome.…
Answer: How to check Burrows-Wheeler Aligner (BWA) version on my terminal?
by
Dave Carlson
▴
870
Just run the `bwa` command without the `--version` flag:
> $ bwa
>
> Program: bwa (alignment via Burrows-Wheeler transformation) Ve…
Comment: Why are reads from a region of a gene but not recongined as a mapped reads>
by
Pierre Lindenbaum
147k
why a screenshot of samtools when you can just copy and paste the text. Save the planet.
Comment: error in kmergenie compilation
by
Shakunthala Natarajan
•
0
Thank you for pointing that out. I compiled it and it now works. Thanks a lot!
Comment: Are upset plots bad for differential expression analysis?
by
LChart
▴
380
> Could you elaborate on what do you mean by discordant differential expression?
Significant, but opposite sign.
> provided I find an ele…
Comment: AF = 0.5 in chrX, VCF of a male
by
paolo
▴
10
So, can I consider calls like these of good quality and assume the REF allele?
Comment: error in kmergenie compilation
by
GenoMax
118k
As the [**README**][1] says, you have to compile the program before you can use it.
[1]: http://kmergenie.bx.psu.edu/README
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