Blat_with_BAM_output
Blat_with_BAM_output
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Runs Blat with default settings and converts the output to BAM format.
Quick Start
- To use Blat_with_BAM_output, import your data in fasta format.
- Resources: https://genome.ucsc.edu/FAQ/FAQblat.html
Description and Quick Start
This is a workflow between Blat with psl output and SAM to BAM. There is a Blat step, then it uses script to convert psl files produced by BLAT into the SAM file format, and then the SAM file is converted to a BAM file.
Test Data
/iplant/home/shared/iplantcollaborative/example_data/Blat_with_BAM_output
Input File(s)
Input a fasta file, seqret.output
Output File(s)
A SAM file, and a BAM file.
References