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Old 08-22-2011, 05:18 AM   #1
Location: il

Join Date: Jun 2010
Posts: 64
Default Scripture workflow


I would like to use scripture in RNA seq experiments.

I thought of the following work-flow:

1. Align reads with Tophat.
2. For each biological sample separately: run scripture with the segmentation task for each biological sample - separately for each chromosome separately and concatenate the resulting bed files.
3. Run scripture with the toGFF task for each biological sample
4. Rum cufflinks' cuffmerge for the resulting GTF files (one file per biological sample) to obtain one GTF annotated GTF file
5. Use scripture score task with the GTF obtained from cufflinks cuffmerge to get counts for each of the samples.
6. merge the files with the counts and continue to analyze fold changes.

If anyone had the experience to use these tools, will be happy to hear if you have any comments on the work flow.
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