Jens Luebeck jluebeck

## ReactionDiffusionSimulatorDemo.md

      
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                jluebeck
                / ReactionDiffusionSimulatorDemo.md
            
            
              Created
              June 3, 2019 20:40
            
          
Created with ReactionDiffusionSimulator.

  
## unmap_bam.sh
#!/bin/bash

#requires samtools (1.3 or greater recommended)

#assumes you can use 6 threads for sorting! Change -@6 if needed.

#takes as input a single file (as argument)
#outputs 4 fastqs, r1 ("_1.fq"), r2 ("_2.fq"), ambiguous reads - both or neither r1 and r2 (_ambiguous.fq), single ended reads (_SE.fq)


## union_bed.sh
#!/bin/bash

cat $1 | while read f;
do
cat $f >> fullbed.bed
done

sort -k1,1 -k2,2n fullbed.bed > fullbed.sorted.bed
rm fullbed.bed
bedtools merge -i fullbed.sorted.bed > merged_bed_union.bed

## istat_overlap_karyogram_plot.py
#!/usr/bin/env python

'''
 REQUIREMENTS:
 'AA_DATA_REPO' environment variable: https://github.com/AmpliconSuite/AmpliconSuite-pipeline
 'CV_SRC' (cycleviz) environent variable: https://github.com/AmpliconSuite/CycleViz
 matplotlib
 numpy
 intervaltree
	#!/bin/bash

	#requires samtools (1.3 or greater recommended)

	#assumes you can use 6 threads for sorting! Change -@6 if needed.

	#takes as input a single file (as argument)
	#outputs 4 fastqs, r1 ("_1.fq"), r2 ("_2.fq"), ambiguous reads - both or neither r1 and r2 (_ambiguous.fq), single ended reads (_SE.fq)
	#!/bin/bash

	cat $1 \| while read f;
	do
	cat $f >> fullbed.bed
	done

	sort -k1,1 -k2,2n fullbed.bed > fullbed.sorted.bed
	rm fullbed.bed
	bedtools merge -i fullbed.sorted.bed > merged_bed_union.bed
	#!/usr/bin/env python

	'''
	REQUIREMENTS:
	'AA_DATA_REPO' environment variable: https://github.com/AmpliconSuite/AmpliconSuite-pipeline
	'CV_SRC' (cycleviz) environent variable: https://github.com/AmpliconSuite/CycleViz
	matplotlib
	numpy
	intervaltree