module load rclone
rclone copy --drive-shared-with-me "dtigoogledrive:/DR_cellranger test/" .
Looking at DR-9163_25_S25_L001_R2_001.fastq.gz
. See count_gRNAs.R for detail. Executed as:
Rscript scripts/count_gRNAs.R
Briefly, the script
- reads in the sequence-containing rows from the
fastq
file - excludes reads with
N
s (there aren't many anyway) - finds reads with expected pattern of
'GTTG[ACTG]{20}GTTT'
where the gRNA is precisely 20 nt sandwiched betweenGTTG
andGTTT
- matches exctracted gRNA sequence with those expected from
data/adt-tags-183sgRNAsequences-Tian2019.csv
- plots distribution of guides with at least 1 occurence
See table: gRNA_distribution.tsv
cellranger.sh ran on Biowulf with sbatch
. Right click and locally save the web summary here then open in your browser to view.