Failed to replicate results SRX175350

[parveshbarak]

I downloaded SRR641640 run of SRX175350 as a fastq file from NCBI website.
I then used the below set of commands to convert the fastq file to pat format:

1. Index the hg19.fa file
   bwa index -a bwtsw hg19.fa
2. Generate a .sam file using reference and input fasta/fastq files:
   bwa mem reference_genome.fasta input.fastq > output.sam
3. Convert the output.sam file to sorted bam file:
   samtools sort -o sorted_output.bam output.sam
4. Index the sorted_output.bam file:
   samtools index sorted_output.bam
5. Convert the .bam file to .pat.gz format:
   wgbstools bam2pat sorted_output.bam
   The pat file I got should ideally contain all the entries of the pat file provided in the tutorial section of UXM tools for SRX175350. But that was not the case and therefore I also got different results on deconvoluting the pat file.

Attaching the given pat file and output (files starting with name Given_) in the tutorial for SRX175350 and the ones I got (files starting with MyExp_) with SRR641640 run of SRX175350
Given_Lung_STL002.pat.gz
Given_Lung_STL002.pdf
MyExp_Lung_STLOO2.pdf
MyExp_Lung_STLOO2.pat.gz