[billthebrute]

Hi all,

I am having trouble running cufflinks on tophat output from a lane of RNA-SEQ GA-IIx data. Is there a way I can avoid the tool getting stuck with something that has *so many non-redundant alignments*, maybe just ignore that and move on to complete the analysis?

Any comments are appreciated.

$ ../cufflinks-0.7.0.Linux_x86_64/cufflinks -p 2 berg_42R7WAAXX_300164_41.lane1/accepted_hits.sam
...
Processing bundle [ gi|89161199|ref|NC_000002.10|NC_000002:88936024-88936173 ] with 3 non-redundant alignments
Processing bundle [ gi|89161199|ref|NC_000002.10|NC_000002:88936699-88936749 ] with 1 non-redundant alignments
Processing bundle [ gi|89161199|ref|NC_000002.10|NC_000002:88936940-88936990 ] with 1 non-redundant alignments
Processing bundle [ gi|89161199|ref|NC_000002.10|NC_000002:88937389-88942713 ] with 773098 non-redundant alignments
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted

Hi all,

has this problem been solved ? I am having similar difficulties and considering the size of the bundles I do not think it is due to a memory problem. Is there something I can check in the sam files (I can script) to see what is causing the problem ?

Thanks !