R for Data Science

https://r4ds.had.co.nz/


how to get your data into R, get it into the most useful structure, transform it, visualise it and model it.

changing chromosome notation in .BAM file

http://seqanswers.com/forums/showthread.php?t=22504


https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/


change chromosome notation "1" to "chr1"

for file in *.bam; do filename=`echo $file | cut -d "." -f 1`; samtools view -H $file | sed -e 's/SN:\([0-9XY]\)/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - $file > ${filename}_chr.bam; done


for loop

for file in *.bam; do filename=`echo $file | cut -d "." -f 1`; samtools view -H $file | sed -e 's/SN:\([0-9XY]\)/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - $file > ${filename}_chr.bam; done

deepTools: tools for exploring deep sequencing data

https://deeptools.readthedocs.io/en/latest/index.html

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Violinplot for Matlab

https://github.com/bastibe/Violinplot-Matlab

SeqPlots : interactive tool for visualizing track signals and sequence motif densities along genomic features using average plots and heatmaps

https://github.com/Przemol/seqplots

 SeqPlots is a web browser tool for plotting average track signals (e.g. read coverage) and sequence motif densities over user-specified genomic features.

Standalone versions of SeqPlots are available as a Mac OS X (10.6 or higher) app bundle combing R, all required packages and scripts([subproject home]) or as an R package ([subproject home]).