Dear PacBio team,
I have used CA8.1 to assemble pacbio self-corrected sequences. In the wiki of PacBioToCA, it has such "After assembly, polishing with Quiver is recommended to get the final consensus sequence".
In my system, I don't have and can't have SmrtAnalysis or SmrtPortal installed. I installed each program that needed through the progress. For example, I installed BLASR when CA8.1 self-correction needed it. And, I installed Quiver just now.
However, in HowToQuiver, I can't follow Step 3 or Step 4. For step3, since I don't have aligned_reads.cmp.h5, I was trying to find out how to follow the RS_Mapping_QVs protocol. But when I google "RS_Mapping_QVs protocol", all I can get is HowToQuiver.rst. I am in a dead end. For step4, since I don't have and can't have SmrtPortal, I am also in a dead end.
Can you please help me? It seems to me that as long as I can create the aligned_reads.cmp.h5 file, then, I am good to run Quiver. Thanks!
I have used CA8.1 to assemble pacbio self-corrected sequences. In the wiki of PacBioToCA, it has such "After assembly, polishing with Quiver is recommended to get the final consensus sequence".
In my system, I don't have and can't have SmrtAnalysis or SmrtPortal installed. I installed each program that needed through the progress. For example, I installed BLASR when CA8.1 self-correction needed it. And, I installed Quiver just now.
However, in HowToQuiver, I can't follow Step 3 or Step 4. For step3, since I don't have aligned_reads.cmp.h5, I was trying to find out how to follow the RS_Mapping_QVs protocol. But when I google "RS_Mapping_QVs protocol", all I can get is HowToQuiver.rst. I am in a dead end. For step4, since I don't have and can't have SmrtPortal, I am also in a dead end.
Can you please help me? It seems to me that as long as I can create the aligned_reads.cmp.h5 file, then, I am good to run Quiver. Thanks!
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