Mostly zeros in pasite.csv

[rbarbieri86]

Hello,

I have ran SCAPE on the chr5 BAM aligned with STARsolo of a public dataset sample (id: ERR4898566). I have used Gencode M10 annotation for the UTRs and ran apamix with default parameters, however I get only sites with no reads (only zeroes).

The toy example completes its run and produces an output, and I have checked a gene of interest in my BAM to see if any reliable reads were there and that was the case ( a few thousands). Could you help me out?

Thank you in advance!

[zhou-ran]

Hi,

Sorry for the late reply.

The predominance of polyadenylation (pA) sites was recorded as zero, a result of the preliminary classification of pA sites without correlating them to valid cell barcodes. Upon completion of the pA site identification process, cell barcodes not included in the filtered outcomes of the barcode file—representing authentic cells—were omitted. This process resulted in the identification of certain pA sites as zero. You could just filter out the results and move on.

Ran