Bowtie2 mapping command update

[pichaelpayne]

In the Aligning Reads section , the command is listed as:

bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq.gz \
    -2 SRR957824_trimmed_R2.fastq.gz -S SRR957824.sam

However, .gz compressed files were not generated in the previous sections, just flat SRR957824_trimmed_R1.fastq and SRR957824_trimmed_R2.fastq files. So either those files should be gz compressed or the command here updated to :

bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq \
    -2 SRR957824_trimmed_R2.fastq -S SRR957824.sam