cory-weller / pipseq-pilot

PIPseek-validation

Retrieve files from Google Drive

module load rclone
rclone copy --drive-shared-with-me "dtigoogledrive:/DR_cellranger test/" .

Check gRNA distribution

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

1. reads in the sequence-containing rows from the fastq file
2. excludes reads with Ns (there aren't many anyway)
3. finds reads with expected pattern of 'GTTG[ACTG]{20}GTTT' where the gRNA is precisely 20 nt sandwiched between GTTG and GTTT
4. matches exctracted gRNA sequence with those expected from data/adt-tags-183sgRNAsequences-Tian2019.csv
5. plots distribution of guides with at least 1 occurence

See table: gRNA_distribution.tsv

Gene expression: Running Cellranger

cellranger.sh ran on Biowulf with sbatch. Right click and locally save the web summary here then open in your browser to view.