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1500 questions
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How many reads has my sequencing run produced on minion?

I am running a 48 h sequencing protocol on a FLO-MIN107, on MinION, with DNA library-prepped with SQK-RAD004. MinKNOW is installed on my Mac and controlling the MinION. I have found the following histogram in MinKNOW. What do the numbers mean? In…
Biomagician
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1 answer

Difference between 1D and 1D^2 data

I am working on ONT data. Initially, I have worked on data from 1D using Minimap2 aligner. I came across 1D^2 from ONT website. I was wondering how different is the data from two techniques? What is the difference between 1D and 2D? and do we get 2 …
KVC_bioinfo
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Strange per sequence GC content results

I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination and a shift in the curve is suggestive of a…
beginner
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2 answers

How to filter info score post-imputation?

this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation? I did imputation in Impute2 and am planning on using SNPtest to analyze, but cannot tell if I should…
hp2018
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removing indels in plink

I have data in Plink format. I removed Indels using --snps-only command in Plink, but still some snps are as below: rs58119544;rs5746975 0 16915280 T A I wonder, how i can get rid of these snps? the correct should be single snps without…
user2808642
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1 answer

Combine multiple species trees

I have five species trees run using starBeast and Beauti. Here is a link to the paper discussing both, http://journals.plos.org/ploscompbiol/article/file?type=supplementary&id=info:doi/10.1371/journal.pcbi.1003537.s006 Each of these trees has the…
Erin Thompson
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How to read .bwt file .sa file?

In BWA project in bwt.c file I found bwt_dump_bwt method and bwt_dump_sa method. I want to use them to read .bwt file and .sa file. I wrote the following program: int main(void) { char *tmp, *prefix; bwt_t *bwt; prefix =…
Mariam
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Assuming that we have the following SNP and phenotype data, is the SNP significantly associated with the phenotype?

So if I attempt this question using their method I put the data of genotype and phenotype into a data frame in R then use lm() to do linear regression and summary() to get an F statistic with p value 0.54. I'm not connecting what the F statistic…
user2332
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2 answers

Parse BAM by insertion size and get genomic coordinates

I would like to find out where (in genomic coordinates) large insertions are found within a given BAM file, file.bam. (In terms of genomic coordinates, I just mean I would like to have a rough idea where to look at the BAM in IGV, chromosome and…
ShanZhengYang
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What is the standard way to measure contig sequence lengths in a BAM?

What is the standard way to measure contig sequence lengths in a BAM? My understanding is that the community would use samtools idxstats to compute this information from the corresponding index file. Are there more precise/standard approaches?
EB2127
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3
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3 answers

Parsing SAM/BAM files for additional information

I used BWA-MEM to alignment and I would like to gather the some informations like total % of match, mismatch, insert/delete etc. I am wondering if there is any existing tools that produces this information?
viz12
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Does MinKNOW work with Mac OSX high sierra 10.13.1?

I have done a compatibility check as described here on my computer to know if I can use MinKNOW on my mac laptop. It says that my OS is incompatible and that the OSX must be Yosemite or El Capitan. Did anyone manage to make MinKNOW work on High…
Biomagician
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Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein here. The trajectories are from my Gromacs simulation. Firstly I use File - New Molecule... to load the protein.gro file. Secondly I use File - Load Data into Molecule... to load my…
lanselibai
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factoextra: Error in if (xlab == "x") xlab <- "x value" : argument is of length zero

I just followed the tutorial trying to do clustering on my own data, but I can't visualize it because fviz_cluster function is giving me an error: Error in if (xlab == "x") xlab <- "x value" : argument is of length zero Here is the code I am…
Nikita Vlasenko
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How to simulate biological pathways?

I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using differential equations or any other formalism. For…
0x90
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