Stephane Plaisance

Dear, I try to extract fastq reads that start with a 7-base UMI followed by a primer sequence. They should match the regexp **/^[ATGC]{7}GCCCAGGTGCAGCTGCAG/** but it does not work when...

My sample file names are very long and make ugly plot axes. can I plot using a different metadata column for names (eg sample_id or paste0(group, "-", replicate) from the...

circos plot or matrix reporting combinatorial usage of V and J chains (D?)

2

## 🚀 Feature a function producing matrices or circos plot for a given sample with the different V-J combinations as edges and number of clones/reads as weight as done in...

## 🐛 Bug "Plot to R console" does not seem to bring the resulting code back to the RStudio Rscript ## To Reproduce Steps to reproduce the behavior: 1. open...

use circlator to fix mitochondrial contig only from canu assembly

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Can I apply circlator to the faulty Mt contig which is present as a partly self overlapping duplicated sequence resulting from assembling the circular chromosome? I have already assembled using...

PlotFancyVJUsage error during ploting

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I could run the tool last week but after some updates it now fails, probably due to circlize below is the result of running the command which creates the txt...

Thanks for the great tool! I have input with pipe symbols which are later interpreted as column delimiters. would be cool to have the option to escape them during conversion.

fefature req: filter database by file extension

5

I would like to get the picture of disk occupancy for a given file type(s) which I know are large and could be removed to recover space. Is there a...

I would like to do the reverse of slop and get the coordinates with negative -l and -r values. ie. enter N bases at both ends. Besides using Awk is...

Can this be done at all (I am working with Saccharomyces right now)? I edited the config.yml to match my paths After failing with the default command `snakemake all --config...