Sometime ago, I wrote a blog about how to convert Eland sorted.txt file to bam file
convert Eland sorted.txt to bam file
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 My first try on Git)
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 SRA file and my first Bowtie run on UF HPC (high performance computing center) 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