Mapping

[jingyayeah]

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]

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

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#21, or mute the thread
https://github.com/notifications/unsubscribe-auth/ALL2zYTor6ZHJhRMIjIPEVo66wLAOFU7ks5qYX8WgaJpZM4JTQ3T
.

[jingyayeah]

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

Best,
Wang