I am planning to use bam2fastx tool for converting the BAM files from PacBio sequencing to fastq. (I prefer a command line tool over SMRT link). However, I cannot find any manual for this tool.
The help says that there is an option called --split-barcodes for demultiplexing. However, there is no information about the format to provide the barcodes in. My sequencing data contains ~120 asymmetrically PCR-barcoded samples. How do I split the data into multiple files using this tool?
Documentation for the commands can be found in the official SMRTanalysis guide. I don't see any way to specify index sequences so it must be recognizing official PacBio indexes. There is one more page here.
The SMRT link user guide says that the barcodes should be provided in a csv format. Do you think this tool would use the same format?
I tried running --split-barcodes without any argument (not sure if it takes any argument) and it gave an error: subreads.bam has no barcoding data
I just found that there is another application for demultiplexing: lima
Trying. Reading the documentation. Will update.
Hi Were you able to demultiplex the PacBio data? If yes how. I am struggling as well.
Yes. I used lima and it worked quite well. However, I am not sure if the SMRT tools package is the same or if they have done major updates.
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