anyone who has experience use TopHat to analyse data from RNA seq?
i have 2 questions here.
1. Which output file in TopHat can be used to mining SNPs
using SAMTools. Is that acceptedhits.bam?
i'm a beginner in analyzing RNA seq so there's a liltle bit confuse for me to understand the output from TopHat. Infact I'm using RNA seq to mining the SNPs.
2.what also we can do with junctions.bed data? do we need to map back the unmapped reads from bowtie to junctions.bed?
thanks!
i have 2 questions here.
1. Which output file in TopHat can be used to mining SNPs
using SAMTools. Is that acceptedhits.bam?
i'm a beginner in analyzing RNA seq so there's a liltle bit confuse for me to understand the output from TopHat. Infact I'm using RNA seq to mining the SNPs.
2.what also we can do with junctions.bed data? do we need to map back the unmapped reads from bowtie to junctions.bed?
thanks!
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