ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
Hi,
the input barcoded txt file has the same barcodes with my data, but the position x,y was not matched my data. For example, the barcodes with the positon x50, y 1 in the file, but this barcode sequence in my fastq data would be x20, y 25. I have successfully run the pipeline but lots of the reads were filtered during the aglinment. Do you think the barcode positon would be the reason?
Hi, the input barcoded txt file has the same barcodes with my data, but the position x,y was not matched my data. For example, the barcodes with the positon x50, y 1 in the file, but this barcode sequence in my fastq data would be x20, y 25. I have successfully run the pipeline but lots of the reads were filtered during the aglinment. Do you think the barcode positon would be the reason?