bedtools Posts

C: Assembly gene prediction/annotation of plant mitochondria by Vijay Lakhujani ♦ 3.4k
Good suggestion. Done !
C: Assembly gene prediction/annotation by toralmanvar • 710
I think you should frame your question to include word "plant mitochondria", so that people can s...
C: Assembly gene prediction/annotation by toralmanvar • 710
That's for assembly and not annotation.
A: Assembly gene prediction/annotation by toralmanvar • 710
You can use [Geseq][1] which is web based tool and easy to use. It works well with both mitochond...
C: Failed to populate reference for id 1? by finswimmer ♦ 7.8k
Hello again, no I haven't found any source for this information. It was more an interpretation o...
C: Pilon polishing highly repetitive nanopore assembly by WouterDeCoster ♦ 35k
Thank you for your well-written and detailed question. I have slightly adapted your title to make...
C: Parsing error with Provean : Someone else ? by jsgounot • 130
Sorry, really old topic and when I look at what I wrote at that time about this, I think I just g...
C: Analysis Without Replicates by ATpoint ♦ 10k
In case the shrinkage does not give satisfying results and you have to use unshrunken FCs, I woul...
C: RNA-strandness of single cell library prep methods by Juke-34 • 1.7k
I guess yes firststrand (RF) sound the one to use.
C: GATK best practices for Broad-produced NGS data by Mehulsharma.253 • 0
Thank you ! GATK forums seems to be having some issues with enabling posting and commenting becau...
C: Analysis Without Replicates by kristoffer.vittingseerup • 980
Sounds like a good plan, especially with the log2FC shrinkage - just remember log2FC != pvalues
A: Could you please tell me how should I analyze the difference between KO and WT m by kristoffer.vittingseerup • 980
I highly recomend Seurat to do the analysis downstream of quantification - it is easy to use, fas...

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