Extracted Barcode in lr_bc_matches does not match queried Barcodes

[jkbenotmane]

Hello,
I was testing scTagger with 10X Visium Data and was a little confused by the Output of "match_lr_bc-trie.py".
What are the Column Names for the Output? I assumed it should be: ReadID, Edit Distance, Strand, Adapter, Barcode, is this correct ?

How come it matches Barcodes, that are not in the short reads ? Are those the error riddled Barcodes from the read itself or how to understand this ?
Is there any order in the matched barcodes separated by ',' or are they all equally good matches ?

[ghazaleb75]

Hi,
The output of "match_lr_bc-trie.py" is:

• First column: Read id
• Second column: Minimum edit distance
• Third column: Number of short reads barcodes that match with the long read
• Fourth column: Long-read segment
• Fifth column: List of all short-read barcodes with minimum edit distance (without any order)

[jkbenotmane]

Thanks for clarifying !

I also wondered why I see barcode marchds in the final output file that are not in the queried sr-bc file ? Where do they come from ?

[baraaorabi]

Can you check if the extra barcodes are just the reverse complement of existing barcodes? it's probably that

[jkbenotmane]

Hi, I checked for forward, reverse, complement and reverse complement and indeed all bcs are now found.

Is there any reason why not only the matching input barcodes are reported by scTagger ?
I just think it Would make analysis later on easier and more straightforward.