Which files from PacBio output files to use in downstream analysis in R
I just received Pacbio sequences of 16S gene from the core facility. After download, I got 5 files for each sample with following suffix:
.ccs.bam
longest.bam
scraps.bam
subreads.bam
whitelist
From readings, I believe that I should start with ccs.bam files (demultiplexed aligned sequences) and convert them into fastq files for downstream analysis in R using DADA2 package, correct?
I installed bam2fastq on my Linux machine, and I am writing this post asking for support including links and materials about the protocol of what to do next.
Thanks!
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