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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Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.

BLAT_psl_to_SAM

### 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