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==Analysis== *Running bowtie alignment on previous down-sampled datasets and transform the output to sam-format **Using samtools to convert the output from sam-format to bam-format and then to pileup-format. **Script: fastq2pileup-hc2 **Data resource: down-sampled raw reads (meet 1,000,000 unique mappable reads): e.g. s_4_ID1_cut_2262955.txt **Template:E.coli-k12-mg1655 template **Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals **Output the data: e.g. s_4_ID1_cut_2262955.bowtie.pileup *In UNIX, extract data from column 1, 2 and column9 with "^" symbol ("^" read starting sign in pileup-format) from each line **Output the data: e.g. s_4_ID1_cut_2262955.bowtie.pileup.readstart *Using perl to calculate "^" symbol in defined bin size (10,000 bp) **Script: CountReadStart-hc2 **Output the data: e.g. s_4_ID1_cut_2262955.bowtie.pileup.readstart.count *Use excel to plot the Read-start counts vs. bin numbers (genome position)
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