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Old 05-18-2010, 09:21 PM   #1
repinementer
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Location: asia

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Default how to check the quality of RNASEQ data

Hi guys I just started RNASEQ analysis. Seems so much going on here! :P. Lot's to catch up!
I have currently ABI Solid RNASEQ sequencing results with me. Would you please tell me what are the basic things to done first.

I'm thinking to check the quality of tags first
and then use BOWTIE and TOPHAT and CUFFLINKS ?

Thanx a tone who ever answer my naive question
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Old 05-18-2010, 11:09 PM   #2
repinementer
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Default sorry for naive question

Sorry some one already had a nice discussion in this site.
Awesome!!!! This is the order but I don't have any answer for 1st step?

1. normalize reads [ used ? ]
2. map reads back to genome [Tophat-Bowtie]
3. measure expression [ RPKM (DEGSeq) or FPKM measurement (CuffLinks) ]
4. find differential expression [DeSeq, DEGSeq, CuffLinks]
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