I am a newbie into PacBio sequencing. I currently have data from a targeted sequencing study of a specific transcript.
What we have is data from 3 groups of individuals (10-homozygous resistant, 10-susceptible and 10-heterozygous for gene A).cDNA of transcript for gene A was PCR amplified for each individual and barcoded specifically for each individual (total 30 unique barcodes). We then did PacBio sequencing on the PCR product after pooling it. Raw data produced reads that were expected size and also huge number of shorter reads half the size.
I am now trying to figure out what the best approach is to analyze the data in order to obtain all variants forms of this transcript A from each individual.
Would it be better to run LAA or ROI analysis after splitting the reads based on barcodes? Also, how do I capture all the reads for this analysis (as shorter reads seems to be fragments of this transcript).
Please help...thank you!
What we have is data from 3 groups of individuals (10-homozygous resistant, 10-susceptible and 10-heterozygous for gene A).cDNA of transcript for gene A was PCR amplified for each individual and barcoded specifically for each individual (total 30 unique barcodes). We then did PacBio sequencing on the PCR product after pooling it. Raw data produced reads that were expected size and also huge number of shorter reads half the size.
I am now trying to figure out what the best approach is to analyze the data in order to obtain all variants forms of this transcript A from each individual.
Would it be better to run LAA or ROI analysis after splitting the reads based on barcodes? Also, how do I capture all the reads for this analysis (as shorter reads seems to be fragments of this transcript).
Please help...thank you!
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