Assembly using cufflinks

Question

[Bioinfonext]

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

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

But it did not working. any suggestion?

[GenoMax]

Move all other options before the bam file. TopHat suite programs used to be sensitive to order of things on command line. Be more specific than it did not working in terms of errors you see (if any). -G is not a valid option for cufflinks (if I recall right, should be -g).

[Bioinfonext]

Does it require sorted sam only? or any sorted file format it accept whether it is sam or bam. if it is sam only than please share the samtool command that can extract only mapped read from the alinment sam file.