| ../oly_pacbio_.correctedReads.fasta.gz | |
| Parameters | preset = N/A |
| defaultQV = 20 | |
| isNonRandom = false | |
| removeDuplicateReads = true | |
| finalTrim = true | |
| removeSpurReads = true | |
| removeChimericReads = true | |
| checkForSubReads = true | |
| FASTA | 603105 reads (2821269801 bp) |
| 0 reads (0 bp) were short and not loaded | |
| FASTQ | 0 reads (0 bp) |
| 0 reads (0 bp) were short and not loaded | |
| 603105 reads (2821269801 bp) loaded, 0 reads (0 bp) skipped, 0 warnings | |
| trimming/oly_pacbio_.gkpStore | |
| readsLoaded | 603105 reads (2821269801 bp) |
| readsSkipped | 0 reads (0 bp) (read was too short) |
| warnings | 0 warnings (invalid base or quality value) |
No statistics available for store 'trimming/oly_pacbio_.ovlStore'.
| PARAMETERS | |
|---|---|
| 1000 | reads trimmed below this many bases are deleted |
| 0.0450 | use overlaps at or below this fraction error |
| 1 | break region if overlap is less than this long, for 'largest covered' algorithm |
| 1 | break region if overlap coverage is less than this many read, for 'largest covered' algorithm |
| INPUT READS | ||
|---|---|---|
| reads | bases | |
| 603105 | 2821269801 | reads processed |
| 0 | 0 | reads not processed, previously deleted |
| 0 | 0 | reads not processed, in a library where trimming isn't allowed |
| OUTPUT READS | ||
| reads | bases | |
| 474695 | 2067034122 | trimmed reads output |
| 57213 | 285060868 | reads with no change, kept as is |
| 32093 | 66698380 | reads with no overlaps, deleted |
| 39104 | 93466994 | reads with short trimmed length, deleted |
| TRIMMING DETAILS | ||
| reads | bases | |
| 392462 | 160713464 | bases trimmed from the 5' end of a read |
| 367569 | 148295973 | bases trimmed from the 3' end of a read |
Image 'trimming/3-overlapbasedtrimming/oly_pacbio_.1.trimReads.inputDeletedReads' is empty. Probably no data to display.
Image 'trimming/3-overlapbasedtrimming/oly_pacbio_.1.trimReads.inputNoTrimReads' is empty. Probably no data to display.
| PARAMETERS | |
|---|---|
| 1000 | reads trimmed below this many bases are deleted |
| 0.0450 | use overlaps at or below this fraction error |
| INPUT READS | ||
|---|---|---|
| reads | bases | |
| 531908 | 2661104427 | reads processed |
| 71197 | 160165374 | reads not processed, previously deleted |
| 0 | 0 | reads not processed, in a library where trimming isn't allowed |
| PROCESSED | ||
| reads | bases | |
| 0 | 0 | no overlaps |
| 1912 | 5844753 | no coverage after adjusting for trimming done already |
| 0 | 0 | processed for chimera |
| 0 | 0 | processed for spur |
| 529996 | 2655259674 | processed for subreads |
| READS WITH SIGNALS | ||
| reads | signals | |
| 0 | 0 | number of 5' spur signal |
| 0 | 0 | number of 3' spur signal |
| 0 | 0 | number of chimera signal |
| 491 | 497 | number of subread signal |
| SIGNALS | ||
| reads | bases | |
| 0 | 0 | size of 5' spur signal |
| 0 | 0 | size of 3' spur signal |
| 0 | 0 | size of chimera signal |
| 497 | 194985 | size of subread signal |
| TRIMMING | ||
| reads | bases | |
| 240 | 660327 | trimmed from the 5' end of the read |
| 253 | 708286 | trimmed from the 3' end of the read |