BAM from Bioscope in Cufflinks 0.9.x

[AdamB]

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?

[Pejman]

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.

[AdamB]

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.

[DerSeb]

Hello,

I would use TopHat 1.1 and subsequently Cufflinks.

Best,
Sebastian

[AdamB]

..........

[DerSeb]

Hey James,

which files are you trying to analyze?

Best,
Seb

[DerSeb]

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!

[AdamB]

thanks Seb