rrwick
none barcode
Hi,
Normally, I have no problem with Porechop. But on my multiplex cDNA run (SQK-LWB001 same barcode than BC, I have checked on nanopore site), Porechop find 0 barcode, it should find BC01 and BC02. I have tried with parameter less stringent but the result is the same. Do you have any idea ? Moreover, when I do a grep on BC01 or BC02, I have some reads! So I don't understand.
The log is :
Best
read Best
start read end
Set %ID %ID
SQK-NSK007 83.9 79.2
Rapid 69.0 0.0
SQK-MAP006 96.6 100.0
SQK-MAP006 Short 81.5 79.2
PCR adapters 1 100.0 100.0
PCR tail 1 92.9 93.1
PCR tail 2 93.3 89.7
1D^2 part 1 75.9 75.0
1D^2 part 2 79.4 75.8
Barcode 1 (reverse) 100.0 100.0
Barcode 2 (reverse) 92.0 100.0
Barcode 3 (reverse) 75.0 76.9
Barcode 4 (reverse) 80.0 76.9
Barcode 5 (reverse) 76.9 84.0
Barcode 6 (reverse) 80.0 80.8
Barcode 7 (reverse) 76.9 76.0
Barcode 8 (reverse) 80.0 75.0
Barcode 9 (reverse) 75.0 79.2
Barcode 10 (reverse) 77.8 76.9
Barcode 11 (reverse) 79.2 76.9
Barcode 12 (reverse) 80.0 80.0
Barcode 1 (forward) 100.0 100.0
Barcode 2 (forward) 100.0 100.0
Barcode 3 (forward) 76.9 84.6
...
Trimming adapters from read ends
SQK-MAP006_Y_Top_SK63: GGTTGTTTCTGTTGGTGCTGATATTGCT
SQK-MAP006_Y_Bottom_SK64: GCAATATCAGCACCAACAGAAA
PCR_1_start: ACTTGCCTGTCGCTCTATCTTC
PCR_1_end: GAAGATAGAGCGACAGGCAAGT
PCR_tail_1_start: TTAACCTTTCTGTTGGTGCTGATATTGC
PCR_tail_1_end: GCAATATCAGCACCAACAGAAAGGTTAA
PCR_tail_2_start: TTAACCTACTTGCCTGTCGCTCTATCTTC
PCR_tail_2_end: GAAGATAGAGCGACAGGCAAGTAGGTTAA
BC01_rev: CACAAAGACACCGACAACTTTCTT
BC01: AAGAAAGTTGTCGGTGTCTTTGTG
BC02_rev: ACAGACGACTACAAACGGAATCGA
BC02: TCGATTCCGTTTGTAGTCGTCTGT
BC01: AAGAAAGTTGTCGGTGTCTTTGTG
BC01_rev: CACAAAGACACCGACAACTTTCTT
BC02: TCGATTCCGTTTGTAGTCGTCTGT
BC02_rev: ACAGACGACTACAAACGGAATCGA
672,546 / 672,546 (100.0%)
579,661 / 672,546 reads had adapters trimmed from their start (51,131,398 bp removed) 475,782 / 672,546 reads had adapters trimmed from their end (28,130,536 bp removed)
Discarding reads containing middle adapters 672,546 / 672,546 (100.0%)
16,778 / 672,546 reads were discarded based on middle adapters
Saving untrimmed reads to barcode-specific files
Barcode Reads Bases File
none 655,768 299,830,209 none.fastq
Thanks a lot for your help,
Had the same/a similar problem, fixed it by installing the 0.2.4-beta from development branch: e.g. run: pip install git+https://github.com/rrwick/Porechop.git@development
See here: https://github.com/rrwick/Porechop/issues/44#issuecomment-362465575
