Map super-reads and unassembled reads to genome about stringtie

[gpertea]

You can use HISAT (using the -U option) to align the LongReads.fq as single (unpaired) reads. Then you can run HISAT again using the -1 and -2 options to align the two files with paired unassembled reads that have the extension .notAssembled.fq.gz. (please check the HISAT manual about how to perform HISAT searches). After both these HISAT searches are performed, it's important to sort the resulting SAM files by converting them to BAM and sorting each BAM file, then merge the 2 sorted BAM files into one sorted BAM file, which you can finally give to StringTie for assembly (please check the samtools documentation about how to convert SAM to BAM, sort each BAM and merge sorted BAMs).

[tiramisutes]

Ok,thanks