Read processing:
| Total reads: | 107,839,114 |
| Number of reads post-trimming: | 105,521,554 |
| Reads with 0 barcodes (%): | 1.27% |
| Reads with 1 barcodes (%): | 2.87% |
| Reads with 2 barcodes (%): | 5.29% |
| Reads with 3 barcodes (%): | 90.57% |
| Reads with all 3 barcodes: | 93,882,175 |
| Reads excluded*: | 68.09% (63,925,527 out of 93,882,175 reads) |
| Final number of reads: | 29,956,648 |
(Note: An additional 1,868,348 reads were filtered out during barcode identification)
Alignment results (STARsolo):
| Number of input reads |
29,956,648 |
| Uniquely mapped |
66.94% |
| Uniquely mapped within genes (including introns) |
59.06% |
| Uniquely mapped within genes (excluding introns) |
29.64% |
| Sequencing saturation (1 - Numi / Nreads) |
2.78% |
Unmapped/Multimapped reads
- Multimapped (multiple loci): 4.49%
- Multimapped (too many loci): 0.29%
- Unmapped (too many mismatches): 0.00% (0 reads)
- Unmapped (too short): 28.24%
- Unmapped (other): 0.05% (13,963 reads)
- Chimeric reads: 0.00% (0 reads)
Kallisto pseudoalignment:
| Number of input reads |
29,956,648 |
| Percent pseudoaligned |
75.4% |
| Percent pseudoaligned to unique transcripts |
35.3% |
Per-sample summary
| Sample | Total reads | Uniquely mapped (%) – STARsolo | Pseudoalignment (%) – kallisto |
|---|
| humanmouse12pt5KA | 14,924,008 | 69.97% | 76.6% |
| humanmouse25K | 15,032,640 | 63.93% | 74.1% |
Read processing:
| Total reads: | 54,059,802 |
| Number of reads post-trimming: | 52,994,427 |
| Reads with 0 barcodes (%): | 1.22% |
| Reads with 1 barcodes (%): | 2.75% |
| Reads with 2 barcodes (%): | 5.15% |
| Reads with 3 barcodes (%): | 90.88% |
| Reads with all 3 barcodes: | 47,314,508 |
| Reads excluded*: | 68.46% (32,390,500 out of 47,314,508 reads) |
| Final number of reads: | 14,924,008 |
(Note: An additional 929,914 reads were filtered out during barcode identification)
Alignment results (STARsolo):
| Number of input reads |
14,924,008 |
| Uniquely mapped |
69.97% |
| Uniquely mapped within genes (including introns) |
61.81% |
| Uniquely mapped within genes (excluding introns) |
31.07% |
| Sequencing saturation (1 - Numi / Nreads) |
2.01% |
Unmapped/Multimapped reads
- Multimapped (multiple loci): 4.58%
- Multimapped (too many loci): 0.28%
- Unmapped (too many mismatches): 0.00% (0 reads)
- Unmapped (too short): 25.13%
- Unmapped (other): 0.05% (7,222 reads)
- Chimeric reads: 0.00% (0 reads)
Other details
- Average input read length: 128.0
- Average mapped length: 126.08
- Number of splices (total): 2,112,614
- Number of splices (annotated): 2,090,233
Kallisto pseudoalignment:
| Number of input reads |
14,924,008 |
| Percent pseudoaligned |
76.6% |
| Percent pseudoaligned to unique transcripts |
36.0% |
Show kallisto run details
/home/dsullivan/.conda/envs/swiftseq/bin/kallisto bus -i /home/dsullivan/2/swiftseq/20250409_1/swiftseq_pipeline/index.idx -o out_dir/workup/results/output_humanmouse12pt5KA_kallisto_run_1/ -x 0,0,20:0,20,30:0,30,0,1,0,0 -t 12 --paired --fr-stranded out_dir/workup/fastqs/humanmouse12pt5KA_0_R1.filtered.fastq.gz out_dir/workup/fastqs/humanmouse12pt5KA_0_R2.filtered.fastq.gz
Read processing:
| Total reads: | 53,779,312 |
| Number of reads post-trimming: | 52,527,127 |
| Reads with 0 barcodes (%): | 1.32% |
| Reads with 1 barcodes (%): | 2.99% |
| Reads with 2 barcodes (%): | 5.42% |
| Reads with 3 barcodes (%): | 90.27% |
| Reads with all 3 barcodes: | 46,567,667 |
| Reads excluded*: | 67.72% (31,535,027 out of 46,567,667 reads) |
| Final number of reads: | 15,032,640 |
(Note: An additional 938,434 reads were filtered out during barcode identification)
Alignment results (STARsolo):
| Number of input reads |
15,032,640 |
| Uniquely mapped |
63.93% |
| Uniquely mapped within genes (including introns) |
56.33% |
| Uniquely mapped within genes (excluding introns) |
28.21% |
| Sequencing saturation (1 - Numi / Nreads) |
3.55% |
Unmapped/Multimapped reads
- Multimapped (multiple loci): 4.41%
- Multimapped (too many loci): 0.29%
- Unmapped (too many mismatches): 0.00% (0 reads)
- Unmapped (too short): 31.32%
- Unmapped (other): 0.04% (6,741 reads)
- Chimeric reads: 0.00% (0 reads)
Other details
- Average input read length: 128.0
- Average mapped length: 125.54
- Number of splices (total): 1,914,075
- Number of splices (annotated): 1,894,227
Kallisto pseudoalignment:
| Number of input reads |
15,032,640 |
| Percent pseudoaligned |
74.1% |
| Percent pseudoaligned to unique transcripts |
34.7% |
Show kallisto run details
/home/dsullivan/.conda/envs/swiftseq/bin/kallisto bus -i /home/dsullivan/2/swiftseq/20250409_1/swiftseq_pipeline/index.idx -o out_dir/workup/results/output_humanmouse25K_kallisto_run_1/ -x 0,0,20:0,20,30:0,30,0,1,0,0 -t 12 --paired --fr-stranded out_dir/workup/fastqs/humanmouse25K_0_R1.filtered.fastq.gz out_dir/workup/fastqs/humanmouse25K_0_R2.filtered.fastq.gz