[stdout]
Number of fastq units = 1
Sampling reads from: Sample Peak_002_GEX2 in "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/pilot_Apo_Sym"
Sample Peak_002_GEX2 in "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/pilot_Apo_Sym" is a paired-end library!
Potential chemistries: SFRP, SC5P-R2, SC5P-PE, SC5P-R2-v3, SC5P-PE-v3, SC3Pv1, SC3Pv2, SC3Pv3-polyA, SC3Pv3-CS1, SC3Pv3LT, SC3Pv3HT-polyA, SC3Pv3HT-CS1, SC3Pv4-polyA, SC3Pv4-CS1, ARC-v1

Length based filtering for Sample Peak_002_GEX2 in "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/pilot_Apo_Sym"
LengthStats {
    median: {
        R1: 28,
        I1: 10,
        R2: 90,
    },
}
Compatible chemistries: SFRP, SC5P-R2, SC5P-R2-v3, SC3Pv2, SC3Pv3-polyA, SC3Pv3-CS1, SC3Pv3LT, SC3Pv3HT-polyA, SC3Pv3HT-CS1, SC3Pv4-polyA, SC3Pv4-CS1, ARC-v1
Result: SFRP, SC5P-R2, SC5P-R2-v3, SC3Pv2, SC3Pv3-polyA, SC3Pv3-CS1, SC3Pv3LT, SC3Pv3HT-polyA, SC3Pv3HT-CS1, SC3Pv4-polyA, SC3Pv4-CS1, ARC-v1
After length filter: SC5P-R2, SC5P-R2-v3, SC3Pv2, SC3Pv3-polyA, SC3Pv3-CS1, SC3Pv3LT, SC3Pv3HT-polyA, SC3Pv3HT-CS1, SC3Pv4-polyA, SC3Pv4-CS1, ARC-v1

Whitelist based filtering for Sample Peak_002_GEX2 in "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/pilot_Apo_Sym"
{
    FivePrimeR2V3: 0.00229,
    ThreePrimeV3HTPolyA: 0.97331,
    FivePrimeR2: 0.01854,
    ThreePrimeV4CS1: 0.0039,
    ThreePrimeV2: 0.01854,
    ThreePrimeV4PolyA: 0.00469,
    ArcV1: 0.00088,
    ThreePrimeV3CS1: 0.15616,
    ThreePrimeV3HTCS1: 0.15616,
    ThreePrimeV3LT: 0.00202,
    ThreePrimeV3PolyA: 0.97331,
}
Compatible chemistries: SC3Pv3-polyA, SC3Pv3HT-polyA
Result: SC3Pv3-polyA, SC3Pv3HT-polyA
