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Old 05-04-2011, 09:27 AM   #1
waseem
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Location: Urbana

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Default New to RNAseq

Hello
I am new to RNAseq analysis.
Jut got my sequences and I want to start.
I want to allign the reads to reference transcriptome.
Any guidelines or help for a beginner.
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Old 05-04-2011, 07:17 PM   #2
nirvana
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Maybe you could begin with trying some align softwares, such as BWA
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Old 05-09-2011, 07:50 AM   #3
pbluescript
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Watch some tutorial videos at Galaxy:
http://main.g2.bx.psu.edu/
Or, if you're comfortable with the command line, jump right in with something like Tophat.
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Old 05-09-2011, 09:52 AM   #4
ttnguyen
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There is a tutorial for the analysis of RNA-seq data:
http://seqanswers.com/forums/showthread.php?t=7068
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Old 06-17-2011, 10:00 AM   #5
waseem
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Thank you very much.
It helped a lot.
Next I wanted to do is "to identify polymorphisms in arabidopsis genome" and I have paired end DNA sequences. any hint about where to start?
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Old 06-20-2011, 11:46 AM   #6
pbluescript
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The two main programs people use for SNP detection are samtools and GATK. I'd start with reading the manuals for those.
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