I am using hisat2 for RNA seq data i have some queries --
1) There is option --phred33 ----Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines.
Is this means Ididn't have to run trimmomatic and using this score for alignment the selection quality of reads will be phred 33 ? Please explain.
2) Command I am using --
hisat2 -p 24 --dta --known-splicesite-infile splicesites.txt --phred33 -x hg38 -1 31_1.fastq.gz -2 /media31_2.fastq.gz -S H031.sam --summary-file H031_summary.txt --novel-splicesite-outfile H031_outfile --novel-splicesite-infile H031_infile
In H031_outfile file my getting result like
> 1 15037 15795 -
Anyone can explain me how to interpret this result and this result is totally different form tophat junction file or its gives us appropriate information.How can I get the information of reads skipped ?