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Recent Replies
Comment: Extract significant DEGs using Seurat FindConservedMarkers and FindAllMarkers
by
allingt
•
0
In general, you should threshold on the p value that corresponds to the maximum FDR you can accept.
In practice, for scRNA-seq data, many g…
Comment: T cell subtype annotation
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allingt
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I guess reference-based annotation is not an option?
In my experience, visualising the expression of canonical markers (I don't know if CD4…
Comment: count number of polymorphic sites among samples in vcf
by
Ram
44k
I'm not sure if this will work, but you could use `bcftools view` with [include expressions](https://samtools.github.io/bcftools/bcftools.h…
Comment: count number of polymorphic sites among samples in vcf
by
Pierre Lindenbaum
164k
> However, I want to exclude sites where all of the individuals have a single alternative allele (or a mix of either one alternative allele…
Comment: Repeat CT in overrepresented sequences
by
allingt
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0
CT-rich regions in introns have been reported before. At what positions in your reads does it appear? How does it affect their mapping to r…
Comment: Repeat CT in overrepresented sequences
by
GenoMax
146k
> fastqc keeps identifying overrepresented sequences consisting of C and T.
Which read is it located in? `fastqc` is of limited utility wi…
Comment: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
DOBI
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Thank you so much for your response, and apologies for the delayed reply! Your explanation really clarified things—I’ll check out the secti…
Answer: How to find the adapter sequence of an RNAseq dataset?
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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
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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?
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ATpoint
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> 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
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conmul
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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…
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