BabyFrog

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This is a toy exercise data for RNA-seq & ChIP-seq analysis.

Files

Genome Browser

Indexing the Genome

$ bash run-index.sh

#!/bin/bash

## bowtie2
mkdir bt2db
bowtie2-build XENLA_BabyFrog.fa bt2db/XENLA_BabyFrog

## BWA
mkdir bwadb
bwa index -p bwadb/XENLA_BabyFrog XENLA_BabyFrog.fa

## STAR
NUM_THREADS=8
mkdir stardb
STAR --runMode genomeGenerate --genomeDir stardb --runThreadN $NUM_THREADS --genomeFastaFiles XENLA_BabyFrog.fa --sjdbGTFfile XENLA_BabyFrog.gtf+gff3

Mapping

$ bash run-bt2.sh

#!/bin/bash
DB="./bt2db/XENLA_BabyFrog"

for FQ1 in $(ls ./rnaseq/*_R1.fq.gz)
do
  FQ2=${FQ1/_R1/_R2}
  SAM=${FQ1/_R1.fq.gz/}".XENLA_BabyFrog.bt2.sam"
  SAM=$(basename $SAM)
  time bowtie2 -x $DB -1 $FQ1 -2 $FQ2 -S $SAM
done

for FQ1 in $(ls ./chipseq/*.fq.gz)
do
  SAM=${FQ1/.fq.gz/}".XENLA_BabyFrog.bt2.sam"
  SAM=$(basename $SAM)
  time bowtie2 -x $DB -U $FQ1 -S $SAM
done

$ bash run-bwa.sh

#!/bin/bash
NUM_THREADS=4
DB="./bwadb/XENLA_BabyFrog"

for FQ1 in $(ls ./rnaseq/*_R1.fq.gz)
do
  FQ2=${FQ1/_R1/_R2}
  SAM=${FQ1/_R1.fq.gz/}".XENLA_BabyFrog.bwa.sam"
  SAM=$(basename $SAM)
  time bwa mem -t $NUM_THREADS $DB $FQ1 $FQ2 > $SAM
done

for FQ1 in $(ls ./chipseq/*.fq.gz)
do
  SAM=${FQ1/.fq.gz/}".XENLA_BabyFrog.bwa.sam"
  SAM=$(basename $SAM)
  time bwa mem -t $NUM_THREADS $DB $FQ1 > $SAM
done

SAM to BAM

See SAMTOOLS_HowTo