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I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.

Here is my running command:

python scripts/oases_pipeline.py -m 25 -M 29 -o output -d " -strand_specific -shortPaired data/reads.fa" -p " -min_trans_lgth 100 -ins_length 300"

My library is strand-specific and pair-ended with length 67bp. The reads are shuffled as:

>0(left_mate_forwarded)
ACTC...
>1(right_mate_reverse_complemented)
TATA...

I got some transcripts, but are far from the transcripts annotated, also far from the result of Trinity. The longest contig from Oases is ~2500bp (vs. ~10000bp from cufflinks and ~6000bp from Trinity). The N50 value is also low. It only reports 20 contigs those cover full-length of some transcripts from Cufflinks (totally ~4000), while Trinity reports ~650.

The dataset I am using is a subset of S. pombe. Does it matter?

Could somebody help me point out whether something wrong here?

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You mentioned that the result is far from expected--in what way? Is it just the number of transcripts, or the lengths of those transcripts? –  Daniel Standage Jun 8 '12 at 1:41
    
Also, as stated in the FAQ: Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject. I'm afraid if you can't highlight a significant biological component to you question, it's likely to be closed as off-topic. –  Daniel Standage Jun 8 '12 at 1:46
1  
Em, I tried to post to BioStar, but nobody answers me... –  Cai Shaojiang Jun 8 '12 at 3:54
    
Here is the mailing list for Oases, listserver.ebi.ac.uk/mailman/listinfo/oases-users also there is a thread in SEQanswers seqanswers.com/forums/showthread.php?t=3877&highlight=oases some people also have problems to get Oases work. –  friveroll Jun 8 '12 at 6:35
    
Unfortunately, if nobody answered on Biostars, the chance of getting an answer here is very slim indeed … –  Konrad Rudolph Jun 8 '12 at 6:58
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