Hi there,
It is my first post and hope anyone would help me.
I have PCR amplicon which was amplified using mixture of templates with different SNPs. (It is an analysis that is very similar to the phage display analysis using NGS.)
Since it is 1.7kb long, I used Pacbio for sequencing.
Basically I want to get final results with;
1. the clusters of reads which have same SNPs
2. the ratio between the clusters
I used resequencing protocol in BLSR and found just one variant and with rare variant tool, got 3 variants but couldn't get any cluster information and ratio. (I guess I used wrong tools.)
Now I am looking for a tool to get the right answer.
Currently, using RS_Resequencing_ReadsofInsert.1, I got 7,372 ccs reads which have more than 9 pass. Using those, I will try some clustering tools. (but I am not sure I can make it.)
If anyone has experience on this kind of work, please help me out.
Thanks in advance,
It is my first post and hope anyone would help me.
I have PCR amplicon which was amplified using mixture of templates with different SNPs. (It is an analysis that is very similar to the phage display analysis using NGS.)
Since it is 1.7kb long, I used Pacbio for sequencing.
Basically I want to get final results with;
1. the clusters of reads which have same SNPs
2. the ratio between the clusters
I used resequencing protocol in BLSR and found just one variant and with rare variant tool, got 3 variants but couldn't get any cluster information and ratio. (I guess I used wrong tools.)
Now I am looking for a tool to get the right answer.
Currently, using RS_Resequencing_ReadsofInsert.1, I got 7,372 ccs reads which have more than 9 pass. Using those, I will try some clustering tools. (but I am not sure I can make it.)
If anyone has experience on this kind of work, please help me out.
Thanks in advance,
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