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josiegleeson / BamSlam

Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
MIT License
12 stars 4 forks source link

Some guidance on usage #3

Closed callumparr closed 3 years ago

callumparr commented 3 years ago

Hey! nice paper. I wanted to use this script to provide summary statistics of my mapped reads as well and cite your paper. Looking through the Rscript I can see we need to supply the file-path to the BAM file and output directory but there is also an argument flag for type. I was wondering what this was for.

Can we run simply by:

Rscript in.bam out.directory as in arguments are positional or are there flags?

callumparr commented 3 years ago

haha I am stupid I just put my glasses on and saw there is a usage section in the readme. Sorry to disturb.

josiegleeson commented 3 years ago

No worries Callum! Please let me know if you have any trouble running it.