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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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Mapping #21

Open jingyayeah opened 8 years ago

jingyayeah commented 8 years ago

Hi，Qing I have some questions about mapping. Following the article,the unbiased mapping is mapping each end of the paired-end reads to the genome and a dual-filtering scheme is used，so my questions is：

  1. Blat result do not include informations about mismatch position , how to used if for filtering?
  2. Which bam file is used as the input of giremi? (Bowtie ? but there are 4 bam files from 1 sample)

Best, Wang

zhqingit commented 8 years ago

Hi Wang,

In our paper, the double filter mapping with strict criterion is used to get the real SNVs. Actually, we used the combined alignment from both blat and bowtie. However, these steps can be replaced by other methods, such as GATK. You only need a SNVs list to feed GIREMI.

I am not clear why there are 4 bam files. The only bam file GIREMI needs is the one used to call SNVs.

Best, Qing

2016-07-22 19:40 GMT-07:00 jingyayeah notifications@github.com:

Hi，Qing I have some questions about mapping. Following the article,the unbiased mapping is mapping each end of the paired-end reads to the genome and a dual-filtering scheme is used，so my questions is：

  1. Blat result do not include informations about mismatch position , how to used if for filtering?
  2. Which bam file is used as the input of giremi? (Bowtie ? but there are 4 bam files from 1 sample)

Best, Wang

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jingyayeah commented 8 years ago

Hi Qing, I will try to get a SNV list with GATK, thanks

Best, Wang