The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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BLAT_psl_to_SAM

 

Description and Quick Start
This is a script to convert psl files produced by BLAT into the SAM file format. No real quality scores are entered.

Test Data
/iplant/home/shared/iplantcollaborative/example_data/Blat_psl2sam

Input File(s)
Input a PSL file from BLAT

Parameters Used in App
No options are recommended. Don't use these unless you wrote the script!

Output File(s)
A SAM file. Probably no header.

References

http://www.htslib.org/doc/samtools-1.2.html

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