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Recent Replies
Comment: How to choose --mind value for plink SNPs filtering
by
Fabio Marroni
★
2.9k
Did the error message mention --mind? And how many individuals are in your data set? According to the [manual][1] you should set --mind to …
Comment: scATAC-seq workflow
by
bioinformatics.girl
•
0
I've read this. Clearly I'm looking for a straightforward step-by-step clarification of the processing. Starting from my data that I briefl…
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
•
0
To be honest, i wanted to know only **which type of change**. since you mentioned about the specific exons, if it is possible i wanted to k…
Comment: scATAC-seq workflow
by
Pierre Lindenbaum
152k
> if anyone could provide a straightforward workflow
https://www.frontiersin.org/articles/10.3389/fcell.2022.981859/full "scATACpipe: A …
Comment: DESeq2 results function runs very slow on Windows 10
by
i.sudbery
16k
This would also explain the performance difference - the code is running on multiple cores on the Apple, but only a single core on Windows.
Comment: RNA Editing data from RNA-seq
by
i.sudbery
16k
You usually need DNA sequencing data as well as RNAseq data to identify RNA editing events.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
i.sudbery
16k
What do you mean be "most frequent alternative splicing event"? Do you mean which type of change (cassette exon, alternative 5' splice-site…
Comment: High downstream gene expression
by
i.sudbery
16k
I don't see genes in this location on the standard sheep genome either. The image you've included above doesn't show the gene annotation. B…
Comment: f-index in treemix
by
kk.mahsa
▴
140
I found the answer and I share it with you.
setwd("directory/of/Treemix/results")
source("plotting_funcs.R")
get_f("…
Answer: Can Singularity be installed on a single-node server or does it have to be HPC?
by
ATpoint
68k
It's not the hardware setup (HPC, workstation, laptop, single-node server) that determines what can be installed or not, but the operating …
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
This isn't a matter of "know[ing] the inner workings of PLINK2". It's about clear communication and debugging practice.
You never posted …
Comment: SNP calling
by
Fabio Marroni
★
2.9k
No idea about the first error. I rarely used GATK, but I have a guess regarding the second error. 1) emit-ref-confidence = ERC, 2) the soft…
Comment: snakemake Unexpected keyword bam in rule definition
by
Aidand
•
0
I'm running version 7.18.1, the first line is missing a \ at the beginning but the first section of the file is just for setting up a log f…
Comment: Network analysis for two Factors
by
Ankit
▴
390
Hi.
Thanks for the response
I tried to use gephi and cytoscape but since I have no experience with these tools I could not use it pro…
Answer: Virtual box
by
ATpoint
68k
Don't struggle with virtual machines. Use awindows Subsystem For Linux (WSL2) to habe a native Linux running within Windows. It's from Micr…
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