Open jingyayeah opened 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:
- Blat result do not include informations about mismatch position , how to used if for filtering?
- 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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Hi Qing, I will try to get a SNV list with GATK, thanks
Best, Wang
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:
Best, Wang