Debarcoded Sequences

[ozgegizlenci]

Hello,

I am quite new to sarlacc package. I would like to subset the sequences which carry the same barcodes into seperate folders. However, I couldn't figure out in which step it can be possible.

According to you example;

After adapterAlign and barcodeAlign, I checked as.data.frame(debarcoded@listData) and
as.data.frame(out@listData). None of them had the corresponding barcodes per sequence. Do we have to merge the listData file at this point before going to filteredReads and later realizedReads to get each sequence with barcodes?

Thank you

[LTLA]

Some dredging of my memory suggests that realizeReads() is necessary to pull out the sequences. This is because the sequences are never fully read into memory at any point, we just stream from the file and process reads one at a time to reduce RAM usage (e.g., when processing large multiplexed libraries). So the read sequences are never stored in any of the objects. If you want them, you have to pull them out ex[;ocot;u with realizeReads() (which "realizes" them in memory).