SUPPLY THE STEP OF FILTER

[rpghjs]

Hi,
When i running the step of PASCALL,I saw the ployaDB in optional.So So I didn't choose that option.Now i have a problem that I have a huge amount of data to sift through right now (with 70,000 PASs).How can i use the polyaDB to filter the data via myself instead of running PAScall.

[liguowei-CAS]

Hi,
In the PAScall step, SCAPTURE will generate three BED files for exonic, intronic, 3primeExtended poly(A) sites, which were named as "Your_Output_Prefix.*.peaks.annotated.bed".

SCAPTURE could solely run the "evaluate process" with files mentioned above and polyADB hg38 file with comands below:

/picb/SCAPTURE-main/scapture_evaluate --peak Your_Output_Prefix.exonic.peaks.annotated.bed -o Your_Output_Prefix.exonic.peaks --species human -g /Your_Path/hg38.fa --polyaDB /Your_Path/polyaDB_file --path /picb/SCAPTURE-main/

We take exonic poly(A) sites BED file as an example here, which could be replaced by "intronic.peaks.annotated.bed" and "3primeExtended.peaks.annotated.bed" files.

Then, the output of "scapture_evaluate" step will be "Your_Output_Prefix.exonic.peaks.evaluated.bed", and could directly be applied to the downstream PASmerge or PASquant step.