I want to run FastQ Screen on CyVerse and I don't quite understand the parameters of this app even after looking them up on google. The parameters include:
- 'Aligner' (BOWTIE2, BOWTIE, or BWA)
- 'Subset' (you're supposed to type in a number. Default = 100000)
- Check box 'Illumina v1.3 format (Older format)'
I don't get #2 and #3. Here is the link to the instructions provided by CyVerse on how to run FastQ Screen using sample data https://cyverse.atlassian.net/wiki/spaces/DEapps/pages/241881853/Fastq-screen-0.11.1 Their explanation on parameter #2 and #3 are not very clear to me. I could not find any other source that talks about FastQ Screen parameters without using command line.
Can someone please help me with this?