How to RUN pipeline with MinION fastq file

[sekhwal]

Hi,
I have one fastq file (MinION) and a reference file. I am looking to align with HISAT2. Please suggest a example command to perform the analysis.

Here is my fastq file contains:

@ID_37312
ATTGTTGCGCTGTTAGAATTTAAAAGATTTGATTCCTTACCAATAATTATTTTTTCCGCATTAATTTCAATAGCAGAACAAATTTTGTTATTTTTAAAAC
+
AAFFAFFJJJ7AFJJJFFAFJJFJJFAJ-F7JFJ<FJJJ7FFJFFJJJ7FAJFJJJJJJFJJJJF--FAFJJFJJFJF<JJJJJJJJ<FFA7A<FJJJJ<
@ID_37313
ATTGTTGCGCTGTTAGAATTTAAAAAAGAAATAATTCGTAGATATTACCCAACAATAGTGAATTATCAACAAGATAAGACTCCAAAAAGTTATGTTAATC
+
AAFFFFFJJJFJJAFJ7<FJ<AFFFJFJ<FJJFFJJJJJJ<AJJFJFJ7-<AFAF<AJFJAA7FFJF<JJFJFFJFFFFFAFF<FFJFF<<FAFJJFFJF