I am using this command to do assembly of mapped read on reference genome using the hisat2:

/home/yog/software/cufflinks-2.2.1.Linux_x86_64/cufflinks -g gene.gtf -p 8 -o /data/SNU_work/Analysis/unmapped/unmapped/hisat2/assembly/ mapped.bam

I have few queries:

1) Does it (cufflinks) require sorted bam file or output bam file of hisat2 can be used directly.

2) Can I set minimun assembled contig length 500 bp?

3) cufflinks requires only gtf (annotation file) and bam file.