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Friday, June 7, 2013

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

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:

so, the bamtools (yes, github again...that's why I want to learn git a little bit, see my last post

and picard 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  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

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