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R Bioinformatics GWAS

5 days ago by carlopecoraro2 ★ 2.4k

1 result • Page 1 of 1

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Comment: SPAdes error: finished abnormally, OS return value: 21

Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres

Comment: unicycler error : [Errno 13] Permission denied:

Answer: SPAdes error: finished abnormally, OS return value: 21

Comment: SPAdes error: finished abnormally, OS return value: 21

Removing UMI with UMI tools?

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Popular Question to RNAseqer ▴ 250

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Recent Replies

Comment: bwa mem hangs after a few thousand reads by GenoMax 136k

> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …

Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GeneBC12 • 0

Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…

Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0

Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…

Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k

Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…

Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k

I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…

Comment: frequency plot for peaks by Ankit ▴ 400

what is your txdb? can you explain your experiment in detail?

Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k

paste the file in csv format and a R wizard might come along and help :)

Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k

Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…

Comment: Generate Read counts from bam file by ATpoint 78k

It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …

Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by ATpoint 78k

DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…

Comment: p-value combination methods by dsull ★ 5.0k

Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…

Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by RNAseqer ▴ 250

Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…

Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by Nitin Narwade ★ 1.5k

Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…

Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10

Thanks colindaven!

Comment: Generate Read counts from bam file by Enrique • 0

Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …

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