I read on Cufflinks man page that input sam file, coming from others mappers than TopHat, must be sorted this way:
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
However, it is taking ages, and eventually causes the server on which we are doing calculations to crash. Is there any possibility to achieve the same sorting as Cufflinks wants, overcoming this sorting step? I tried samtools sort, but apparently it is not what Cufflinks needs.
Just in case, I also have alignments with STAR and MapSplice, both of them are also apparently "too big" to be handled by sort as cufflinks wants it. If you are wondering why I am not using TopHat for alignment, well you probably don't even imagine how it is slow for alignment. :P
If you have a valid alternative to Cufflinks, I am also open to new software.
Thanks in advance!