we have used
pacbio technology to sequence our samples (which is only one gene). after demultiplexing and using
ccs tool, now we have one
ccs.bam file per sample.
but we would like to collapse all the sequences (from the same sample which are now in the same
.ccs.bam file) into one sequence which will be used for the downstream analysis.
do you have any experience about the tools and method that we can use.
Are you sure that is correct? Documentation for the
ccstool (LINK) seems to indicate that you should get HiFi consensus reads.
GenoMax yes you will get the consensus sequence. that is in bam format. if you convert it to fasta you will see there are multiple entries. meaning there are many sequences. my goal is to get only one (consensus) sequence.
But the schematic seems to show a single consensus being called. Guess that is not correct? You did use the
subreads.bamfile as input, correct?
GenoMax yes subreads.bam is the input for ccs tool.