Hello!

 

I convert SOLiD csfasta- and qual-files to fastq-files and map those against
Hg19 (Bowtie).

I would like to use the resulting sam-files in the IGV browser (Broad
Institute).

Therefore, the sam-file need to be sorted an indexed. This could be done
using the “igvtools”.

However, it would be nicer if this sorting and indexing could be done
automatically using GALAXY.

I guess that it is certainly possible – but I do not know how.

Could anybody let me know how it works and what function I have to use,
respectively?

How can I sort the sam-file the correct way?

 

Thank you in advance.

 

Best regards

 

Jo

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