Read1/Reads2 using in Kraken2Uniq

[oyxf]

Thank you for the good tool . I have a question to ask you for help, when using Kraken2Uniq to mapping , which reads should be choose for 10x genomics data? Both or only read2? The read1 only contains the barcode and UMI. I see the tool will filtered reads by mapping result, so does it affect the result if I use the both reads ?

[sjdlabgroup]

Thanks for your comment! You can use both reads as input to Kraken, but make sure the "--paired" flagged is used. This will make it easier for you to match barcodes from read1 to reads from read2 from the output of Kraken.

[Yunuuuu]

But if we should run read1 with extract_microbiome_reads.r (which should be just barcode + UMI sequence)?