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Recent Replies
Comment: Snakemake expand(): using a helper function (zip) and imputing wildcards?
by
Jesse
▴
850
Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
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
by
allingt
•
0
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
•
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
•
0
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?
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…
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