I have RNA-seq data for a specific cell line. I also have a specific sequence of interest. I map RNA-seq reads to the sequence of interest using bowtie and generate a .sam file:

First I build an index for my sequence:

bowtie-build campy.fa campy

I then map the reads:

bowtie -s -p 2 campy campy-pre-1m.fastq campy-pre-1m.sam

After generating a .sam file I sort it and then try to use cufflinks to quantity the expression level.

sort -k 3,3 -k 4,4n campy-pre-1m.sam > campy-pre-1m.sam.sorted
cufflinks -o campy-pre-1m.cufflinks campy-pre-1m.sam.sorted

Im getting the following error when I use cufflinks : Cufflinks requires that if your file has SQ records in the SAM header that they appear in the same order as the chromosomes names in the alignments. If there are no SQ records in the header, or if the header is missing, the alignments must be sorted lexicographically by chromsome name and by position.

Since Im not mapping my reads to a genome but only to a 4000 nucleotide sequence which is located on chromosome 12, is there a way to use cufflinks with out sorting since I don't really need to sort anything. Even if i tried to sort first it still doen't work. any help would be greatly appreciated