remap the Eland sorted.txt file from hg18 to hg19

Sometime ago, I wrote a blog  about how to convert Eland sorted.txt file to bam file
http://crazyhottommy.blogspot.com/2013/06/convert-eland-sortedtxt-to-bam-file.html?view=sidebar

the original Eland file was mapped to hg18, but I want to remap it to hg19.

essentially, I need a fastq file to map it by bowtie.

A quick google search:
http://seqanswers.com/forums/showthread.php?t=7061

so, the bamtools https://github.com/pezmaster31/bamtools (yes, github again...that's why I want to learn git a little bit, see my last post http://crazyhottommy.blogspot.com/2013/06/my-first-try-on-git.html?view=sidebar)

and picard http://picard.sourceforge.net/ can do the job.

# you need to module load bamtools in the HPC terminal

$ bamtools convert -in hg18.bam -format fastq > my.fastq

then, I run bowtie as what I did here http://crazyhottommy.blogspot.com/2013/05/sra-file-and-my-first-bowtie-run-on-uf.html?view=sidebar  at UF HPC .

after mapping with bowtie, I got a my_hg19.sam  file, I converted it to bam file and it is ready for downstream analysis.

$ samtools view -bS my_hg19.sam > hg19.bam