Cuffdiff analysis with multiple files

[geneart]

Hello All,
I am trying out cuffdiff and cummeRbund currently and learnt that multiple files can be run to analyse expression. My understanding is that multiple (different samples) can be uploaded to get an expression analysis.
However here is my problem:
I have sample_3 and Sample_7 that I need to compare the expression levels. Sample 3 is a small library so I have one ".sorted" file I could generate by using samtools sort command. However when I sort sample_7 I get multiple " 001.sorted" "oo2.sorted" etc for that library data ,as it is huge!
So if I go further and perform cufflinks or cuffdiff, how can I be sure that the multiple sorted files for Sample_7 is not treated as each new sample to be compared or replicates?
They are neither , they are just the same sample but many files generated while sorting bam.
I dont want this to skew my analysis. Any suggestions?

Thanks
geneart.

[sBeier]

The numbered files you are getting from samtools are only temporary files. They should be cleaned up after the sorting is finished and written into one single sorted file. If sorting does not run any more, but the temporary files are still there, it has exited with an error, maybe because the file is really too big. You can try PicardTools SortSam instead, this one sorts also bigger files.

[geneart]

Thanks very much ! much appreciated,
geneart