Accompanying bash commands

[annajbott]

Hello,

I was wondering if you have example command line commands or bash scripts you used for preprocessing with Kallisto bustools. Thanks!

Best,
Anna

[caleblareau]

Sure! For preprocessing fastqs:

python3 asap_to_kite/asap_to_kite_v2.py -f intracellular_fastqs -s ICA_CKDL240020949-1A -c 12 -o ICA

then

kallisto bus -i feature_reference.idx -x 10xv2 -t 12 -o ICA ICA_R1.fastq.gz ICA_R2.fastq.gz
bustools correct -w 737K-cratac-v1.txt ICA/output.bus -o ICA/output_corrected.bus
bustools sort -o ICA/output_sorted.bus ICA/output_corrected.bus
bustools count -o ICA --genecounts -g FeaturesMismatch.t2g -e ICA/matrix.ec -t ICA/transcripts.txt ICA/output_sorted.bus

does the downstream kallisto/bustools work.