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Recent Replies
Answer: How to find the adapter sequence of an RNAseq dataset?
by
GenoMax
146k
Looks like you are doing this analysis via Galaxy so the following may not help immediately. You can always post to Galaxy help forum for s…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
teofoskol
•
0
There are few ways, but you can't be 100% sure. 1st you can try to normilize with SCTransform (suppossed to remove some of the batch effect…
Answer: filterx : fast and efficient filter tool written in Rust for csv,fasta,fastq,gff
by
dwpeng
▴
100
v0.0.2 has full platform supported now :) !
[https://github.com/dwpeng/filterx/releases/tag/v0.0.2][1]
 (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect?
You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
•
0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data
by
king
•
0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
Chen
•
0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
GenoMax
146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset
by
allingt
•
0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap
by
jared.andrews07
★
18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type
by
allingt
•
0
What do you mean by "significant gene"?
How did you perform GSEA and on how did you rank your genes for it?
From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis
by
allingt
•
0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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