There is typo in code.

[partrita]

[sanbomics_scripts](https://github.com/mousepixels/sanbomics_scripts/tree/main) /simpleaf_alevin_fry_tutorial.txt

simpleaf quant --reads1 a_r1.fastq.gz,b_r1.fastq.gz --reads2 a_r2.fastq.gz,b_R2_001.fastq.gz --threads 28 --index simpleaf_index/index --chemistry 10xv3 --resolution cr-like --unfiltered-pl --expected-ori fw --t2g-map simpleaf_index/index/t2g_3col.tsv --output simpleaf_output

To be

simpleaf quant --reads1 fastq/pbmc_1k_v3_S1_L001_R1_001.fastq.gz,fastq/pbmc_1k_v3_S1_L002_R1_001.fastq.gz --reads2 fastq/pbmc_1k_v3_S1_L001_R2_001.fastq.gz,fastq/pbmc_1k_v3_S1_L002_R2_001.fastq.gz --threads 28 --index simpleaf_index/index --chemistry 10xv3 --resolution cr-like --unfiltered-pl --expected-ori fw --t2g-map simpleaf_index/index/t2g_3col.tsv --output simpleaf_output

[partrita]

also instead of using wc -c command and substrate one manually, this below command will be better way.

gunzip -c fastq/pbmc_1k_v3_S1_L002_R2_001.fastq.gz | head | sed -n '2p' | tr -d '\n' | wc -m