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The inputs into the attach barcode method in the Barcode Platform class include a read 1 fastq (r1), where the cell and molecule barcodes are extracted and an index fastq file (i7, optional), where the sample barcode is distracted.
In order to generalize this class further, is it possible to omit the numerical assignments to the reads. r1 and i1 could become a list of one or more input fastq files, and the tool could enable a user to specify which fastq file the tag should be associated with. These suggestions are from @ambrosejcarr comments and past experiences with In-drop and Mars-seq, where the barcodes are not always in the same positions or on the same fastq files. Please see the following PR where this was discussed...
The inputs into the attach barcode method in the Barcode Platform class include a read 1 fastq (r1), where the cell and molecule barcodes are extracted and an index fastq file (i7, optional), where the sample barcode is distracted.
sctools/src/sctools/platform.py
Line 865 in 09eb7f4
In order to generalize this class further, is it possible to omit the numerical assignments to the reads. r1 and i1 could become a list of one or more input fastq files, and the tool could enable a user to specify which fastq file the tag should be associated with. These suggestions are from @ambrosejcarr comments and past experiences with In-drop and Mars-seq, where the barcodes are not always in the same positions or on the same fastq files. Please see the following PR where this was discussed...
#57
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