Hi,
I am on the new side and am having some trouble with the make.contigs command.
make.contigs(ffastq=Undetermined_S0_L001_R1_001.fastq, rfastq=Undetermined_S0_L001_R2_001.fastq, findex=Undetermined_S0_L001_I1_001.fastq, oligos=oligos.txt):
The files get made alright but when I run summary.seqs it doesn’t look good.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 250 250 0 3 1
2.5%-tile: 1 366 366 0 4 167227
25%-tile: 1 370 370 0 4 1672262
Median: 1 373 373 1 5 3344524
75%-tile: 1 374 374 3 5 5016786
97.5%-tile: 1 378 378 17 6 6521821
Maximum: 1 502 502 50 240 6689047
Mean: 1 373.703 373.703 2.61363 4.74528
of Seqs: 6689047
I have also tried splitting this step up:
make.contigs(ffastq=Undetermined_S0_L001_R1_001.fastq, rfastq=Undetermined_S0_L001_R2_001.fastq)
fastq.info(fastq=Undetermined_S0_L001_I1_001.fastq)
but the result is the same.
We did 251 x 251bp runs using 515f-926r primers. In the past we used different primers so I am unsure if that is the issue or if I need more information in the oligo file:
barcode CAACACATGCTG none P13097
barcode CATACCGTGAGT none P13015
barcode GTCCATGGTTCG none P13289
barcode ACCATTACCATT none P13067
…
Needless to say, if I try filter out anything with a maxambig>0 or that is longer than 275bp, everything winds up in the scrap folder.
Thanks for your help!