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#!/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 |
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#!/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 |
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#!/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) | |