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Old 02-02-2012, 01:17 PM   #1
swapnil2188
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Default Tools or ways to find out variants in RNA seq data ?????

I know that we can find out variants in DNA seq data using different tools(GATK, Samtools..........) but I wonder if there are any tools to find out variants in RNA seq data.

I understand the concept of RNA editing and also the ongoing debate behind it.
Please can anyone help me with how to go with this approach further ?
Also, please suggest me tools to find out variants in RNA seq data
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Old 02-03-2012, 05:22 AM   #2
sdarko
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I believe that you can use GATK and samtools on RNA-Seq data.
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Old 02-03-2012, 05:26 AM   #3
pbluescript
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I've run both GATK and samtools mpileup on RNA-Seq data, and I got better results with samtools. GATK is more geared towards genome SNPs, and I'm sure by playing around with the settings I could get better results with variant calling for RNA reads, but I haven't tried that yet.
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Old 02-04-2012, 02:14 AM   #4
cahillcahill
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you can use GATK
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Old 02-06-2012, 12:03 PM   #5
swapnil2188
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Thanks.............!!!!!!!!!! I guess this might help
I will try both GATK and samtools.

Here a found a list to analyse seq data..........

http://seqanswers.com/wiki/Software/list

I thought this might help as well.....!!!!!!!!!!!
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