I am working with a dataset where the barcodes (CB) and UMIs (UR) are not in the standard string sequence format. Specifically, my barcodes are represented as decimal integers (tag: CB:i:2242) and my UMIs are represented in hexadecimal (tag: UR:Z:7A9EB).
I am writing to ask if velocyto can handle such formats for barcodes and UMIs. If not, are there any workarounds or plans to accommodate these types of formats in the future?
I understand that the SAM specification typically expects barcodes to be in the string format (CB:Z:sequence_of_the_barcode). However, in the case of my data, the non-string representation is crucial and converting to string format would not be ideal.
Here's an example of an alignment from my BAM file:
Hello velocyto maintainers,
I am working with a dataset where the barcodes (CB) and UMIs (UR) are not in the standard string sequence format. Specifically, my barcodes are represented as decimal integers (tag: CB:i:2242) and my UMIs are represented in hexadecimal (tag: UR:Z:7A9EB).
I am writing to ask if velocyto can handle such formats for barcodes and UMIs. If not, are there any workarounds or plans to accommodate these types of formats in the future?
I understand that the SAM specification typically expects barcodes to be in the string format (CB:Z:sequence_of_the_barcode). However, in the case of my data, the non-string representation is crucial and converting to string format would not be ideal.
Here's an example of an alignment from my BAM file:
FP200002485L1C062R04102086386 16 1 3000132 255 100M * 0 0 GACTATTGATGACTGCCTCTATTTCTTTAGGGGAAATGGGACTTTTAGTCCATGAATCTGATCCTGATTTAGCTTTGGTACCTGGTATCTGTCTAGGAAG EGGFG<FAGCGEGEFEEBDEDGEDFEBGHC@CEFDIAC+(DFFFDFFFDDGEFFFFBEFEFFDFFFEDGGGDEDBFD5EDEDEDDDEBEFECCEGDEFED NH:i:1 HI:i:1 AS:i:98 nM:i:0 Cx:i:51152 Cy:i:44492 UR:Z:7A9EB XF:i:2 CB:i:2242Thank you for your assistance and for developing this valuable tool.
Best regards, weir