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Jeffrey E Barrick

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Code Block
cds
cp -r $BI/ngs_course/listeria_RNA_seq/data listeria_RNA_seq

If you want to skip the read alignment step...

To get right to the new stuff you can copy the mapped read BAM files and the reference sequence files that you will need from here:

Code Block

cds
cp -r $BI/ngs_course/listeria_RNA_seq/mapped_data listeria_RNA_seq

Then skip the mapping steps below.

File Name

Description

Sample

SRR034450.fastq

Single-end Illumina 36-bp reads

wild-type, biological replicate 1

SRR034451.fastq

Single-end Illumina 36-bp reads

ΔsigB mutant, biological replicate 1

SRR034452.fastq

Single-end Illumina 36-bp reads

wild-type, biological replicate 2

SRR034453.fastq

Single-end Illumina 36-bp reads

ΔsigB mutant, biological replicate 2

NC_017544.1.fasta

Reference Genome sequence (FASTA)

Listeria monocytogenes strain 10403S

NC_017544.1.gff

Reference Genome features (GFF)

Listeria monocytogenes strain 10403S

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Expand
Just give me the answer...
Just give me the answer...
Code Block
module load bowtie2bowtie
bowtie2bowtie-build NC_017544.1.fasta NC_017544.1

Now create a commands file that looks like this:

Code Block
bowtie2bowtie -p 3 -xS NC_017544.1 -U SRR034450.fastq -S SRR034450.sam
bowtie2bowtie -p 3 -xS NC_017544.1 -U SRR034451.fastq -S SRR034451.sam
bowtie2bowtie -p 3 -xS NC_017544.1 -U SRR034452.fastq -S SRR034452.sam
bowtie2bowtie -p 3 -xS NC_017544.1 -U SRR034453.fastq -S SRR034453.sam

Create the launcher script and run it:

Code Block
module load python
launcher_creator.py -n bowtie -e you@somewhere.com -t 0:30:00
qsub launcher.sge

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