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drmaize / C3S-LAA

Clustering of Circular Consensus Sequences (C3S) for Long Amplicon Analysis of PacBio Data
MIT License
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How to define parameters.py, barcode_info_file if samples already demultiplexed? #1

Open marcomeola opened 5 years ago

marcomeola commented 5 years ago

I have a multiplex run composed of 20 different barcode libraries with all libraries having the same amplicon fragment (same 1st PCR with all the same primers). The sequencing provider sent me the demultiplexed bam files from which I have generated the ccs with the smrtlink-toolkit (ccs: 20 passes + polish).

How do I need to specify in the parameters.py file that I have no h5 files? Does C3S-LAA work with this only ccs or bam files or do I need to get the multiplexed raw bax.h5 file to get C3S-LAA running?

ffrancis commented 5 years ago

Yes, you will need to start with the original multiplexed raw bax.h5 file for C3S-LAA.

On Mon, Mar 11, 2019 at 7:03 AM Marco Meola notifications@github.com wrote:

I have a multiplex run composed of 20 different barcode libraries with all libraries having the same amplicon fragment (same 1st PCR with all the same primers). The sequencing provider sent me the demultiplexed bam files from which I have generated the ccs with the smrtlink-toolkit (ccs: 20 passes + polish).

How do I need to specify in the parameters.py file that I have no h5 files and sequences have no barcodes attached. Does C3S-LAA work with this kind of sequences or do I need to get the multiplexed raw bax.h5 file to get C3S-LAA running?

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marcomeola commented 5 years ago

I was told the sequencing was performed with Sequel and not RS II, which is why there is no bax.h5 file and the bam files are the only output of the raw data, though. So there is not even a multiplexed bax.h5 file. Guess your pipeline will not work on Sequel data, right?