Tophat2 vs HISAT vs STAR

Tophat2 is not bad 
http://cdwscience.blogspot.com/2019/01/tophat-really-isnt-that-bad.html
 
https://genomespot.blogspot.com/2015/03/hisat-vs-star-vs-tophat2-vs-olego-vs.html



Tophat2 is bad
Question: HISAT2 or Tophat2
https://www.biostars.org/p/230724/

bedops --chop : chop bed into identical intervals

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html

The --chop operator merges all overlapping input regions and “chops” them up into a set of disjoint segments of identical length (with a default of one base). One or more input files may be provided; this option will segment regions from all inputs:

Note

Overlapping and nested regions are merged into contiguous ranges before chopping. The end result contains unique, non-overlapping elements.

(base) [lee@ko44 annotation]$ more chrom.sizes.chr.TAIR10.bed
chr1    0    30427671
chr2    0    19698289 
chr3    0    23459830
chr4    0    18585056
chr5    0    26975502

 (base) [lee@ko44 annotation]$ bedops --chop 1000 chrom.sizes.chr.TAIR10.bed > arabidopsis_1kb_chr1_5.bed

(base) [lee@ko44 annotation]$ more arabidopsis_1kb_chr1_5.bed
chr1    0    1000
chr1    1000    2000
chr1    2000    3000
chr1    3000    4000
chr1    4000    5000
chr1    5000    6000
chr1    6000    7000
chr1    7000    8000

 

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]).