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Old 10-04-2010, 03:02 AM   #1
AdamB
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Default BAM from Bioscope in Cufflinks 0.9.x

Is there any documentation on how to use BAM files of SOLiD Bioscope-mapped reads in Cufflinks 0.9.x?

I have run Cufflinks using SAM-converted BAM files with subsequent alterations, but I'm eager to see how it compares using a BAM file as input.

Are there any additional flags necessary to tell Cufflinks about the input file?
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Old 10-04-2010, 06:32 AM   #2
Pejman
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Hi jamessmith01. Did you manage to work out the Bioscope .BAM files + Cufflinks pipeline?
I currently have a hard time choosing a reasonable pipeline for SOLiD csfasta files of a RNAseq experiment.
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Old 10-07-2010, 01:54 AM   #3
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Sorry to bump this thread, but this is a fairly straightforward question, and since I've seen developers lurking, it would be great if someone could answer.

Many thanks.
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Old 10-07-2010, 04:04 AM   #4
DerSeb
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Hello,

I would use TopHat 1.1 and subsequently Cufflinks.

Best,
Sebastian
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Old 10-07-2010, 04:45 AM   #5
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..........

Last edited by AdamB; 10-07-2010 at 04:54 AM.
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Old 10-07-2010, 04:49 AM   #6
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Hey James,

which files are you trying to analyze?

Best,
Seb
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Old 10-07-2010, 04:59 AM   #7
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in case it's rat i would suggest you try tophat since the annotation is not so good. if it's human that problem is not such a big deal!
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Old 10-07-2010, 05:27 AM   #8
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thanks Seb
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