If you just want to extract relevant features like 10x barcode or UMI from fastq data you can process the fastq manually.

For example this will extract the 16-nt 10x barcode from a typical R1 by removing the last 10 characters from the 26-length read

cat Your_R1_001.fastq | \        #cat the R1 and pipe it to awk
awk '(NR%4==2)' | \              #take every 4th line of the fastq starting at line 2
sed 's/.\{10\}$//' > Your_R1.txt #empty the last 10 characters to only keep the 16-nt 10x barcode

If you know the structure of your R1/R2 then you can manipulate them as needed. But as you said, you probably should try a more sophisticated and robust approach

Found a pretty simple solution in the end - using cellranger multi and rerunning my analysis with the CRISPR guides as features