RNA-SEQ with SOLID reads

[dnyansagar]

Hi
I have Solid reads of length 75 x 35
I want to use Tophat and cufflinks to analyze these reads. But the problem is I dont have the fastq files. I have already mapped reads in BAM format.
should I re-run tophat on these mapped reads? and how?
and which library type I should use? and how ?

/dnyansagar

[panagiotis]

Hello, you can try this tool:

http://www.hudsonalpha.org/gsl/software/bam2fastq.php

Be careful though to read carefully the assumtions, and then, when you will run tophat, take into account what is said to the instructions about the Phred scale.

[panagiotis]

Hello, you can try this tool:

http://www.hudsonalpha.org/gsl/software/bam2fastq.php

Be careful though to read carefully the assumtions, and then, when you will run tophat, take into account what is said to the instructions about the Phred scale.

[dnyansagar]

Hello
I have another question. I am new to RNA-seq and therefore the question is sort of basic.
I have Drosophila Solid reads. The experiment have 3 controls (2 wild type and 1 gene specific)and an experiment each having 6 files. I am using Tophat-Cufflinks for the study. My question is, should I use all 18 control files to compare against ?