PacBioToCA
In running pacBioToCA, we found that the amount of PBcR was influenced by the parameter of genomeSize.
Short reads: 100X, long reads: 200X, w/wo genome size
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 miseq.100X.frg.bz2
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 genomeSize=4650000 miseq.100X.frg.bz2
Short reads: 118X, long reads: one ~ four SMRT cell reads, w/wo genome size
| Name | 200X filtered long reads | m120228_192221 | m120228_210845 | Two SMRT cells | Three SMRT cells | Four SMRT cells |
| Filtered_subreads | seqs amount:383482 | seqs amount:38542 | seqs amount:44794 | seqs amount:77117 | seqs amount:113284 | seqs amount:136333 |
| seq avg len:2422.877720 | seq avg len:2322.679985 | seq avg len:2334.414140 | seq avg len:2184.208709 | seq avg len:2333.977711 | seq avg len:2386.664674 | |
| total:929.13 Mb | total:89.52 Mb | total:104.57 Mb | total:168.44 Mb | total:264.40 Mb | total:325.38 Mb | |
| depth: 199.81X | depth: 19.25X | depth: 22.49X | depth: 36.22X | depth: 56.86X | depth: 69.97X | |
| without genome size | ||||||
| seqs amount:332880 | seqs amount:35199 | seqs amount:40811 | seqs amount:64201 | seqs amount:99285 | seqs amount:120296 | |
| seq avg len:2260.68262 | seq avg len:2095.143186 | seq avg len:2086.568670 | seq avg len:2150.165184 | seq avg len:2221.782394 | seq avg len:2252.656963 | |
| total:752.54 Mb | total:73.75 Mb | total:85.15 Mb | total:138.04 Mb | total:220.59 Mb | total:270.99 Mb | |
| depth: 161.84X | depth: 15.86X | depth: 18.31X | depth: 29.69X | depth: 47.44X | depth: 58.28X | |
| genomeSize=4650000 | ||||||
| seqs amount:37879 | seqs amount:34852 | seqs amount:40486 | seqs amount:63411 | seqs amount:70468 | seqs amount:56298 | |
| seq avg len:4927.683492 | seq avg len:2130.841559 | seq avg len:2120.237712 | seq avg len:2198.455315 | seq avg len:2815.903020 | seq avg len:3495.604515 | |
| total:186.66 Mb | total:74.26 Mb | total:85.84 Mb | total:139.41 Mb | total:198.43 Mb | total:196.80 Mb | |
| depth: 40.14X | depth: 15.97X | depth: 18.46X | depth: 29.98X | depth: 42.67X | depth: 42.32X |