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Popular Question to
Alexander
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Popular Question to
Matteo Schiavinato
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Michael Love
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xqyn
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Recent Replies
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…
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
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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…
Comment: Clustering in single cell
by
bk11
★
1.2k
> However, in my analysis, clusters of each cell types are not clearly
> separate even though I tried different clustering algorithms (louv…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
•
0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error:
…
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