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Update README.md #19

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10 changes: 2 additions & 8 deletions README.md
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Expand Up @@ -101,9 +101,9 @@ The previous commands have setup RepEnrich2 annotation that is used in downstrea

After the setup of the RepEnrich2 we now have to map our data uniquely to the genome before running. This is because RepEnrich2 treats uniquely mapping and multi-mapping reads separately. This requires first mapping the data to the genome using Bowtie2, then running the RepEnrich2_subset.py script to segregate the reads into separate files.

First, perform mapping using Bowtie2 (example using paired end data):
First, perform mapping using Bowtie2 and convert the output in bam format with samtools (example using paired end data):

bowtie2 -q -p 16 -x /path/to/annotation/mm9/mm9 -1 /home/Dataset/Sample_L001_R1.fastq -2 /home/Dataset/Sample_L001_R2.fastq -S /home/output/sample_mapped.sam
bowtie2 -q -p 16 -x /path/to/annotation/mm9/mm9 -1 /home/Dataset/Sample_L001_R1.fastq -2 /home/Dataset/Sample_L001_R2.fastq | samtools view -bS - > /home/output/sample_mapped.bam

An explanation of the Bowtie2 options (detailed explanations found [here](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line)):
* `bowtie2 `
Expand All @@ -116,12 +116,6 @@ An explanation of the Bowtie2 options (detailed explanations found [here](http:/

The `.out` file from this run should inform you of the total mapping reads for your alignment



The .sam file should then be converted to a .bam file using Samtools:

samtools view -bS sample.sam > sample.bam

Lastly, the RepEnrich2_subset.py script should be run to output discrete files for uniquely and multi-mapping reads:

python RepEnrich2_subset.py /path/to/sample.bam 30 Sample_Name --pairedend TRUE
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