Long story, but I’m trying to make some recent Miseq data backwards compatible with older forward read data to do some comparisons for a model. Because it’s only forward read, make.contigs will not work (I think), so I’m starting with fastq.info and then trim.seqs. However, I cannot get groups / sample ids into the count table no matter what I try, such as unique.seqs, list.seqs, etc…
So, after I align, screen, etc and get to the end of everything, the results are a single, merged sample with no sample ids rather than results for each site in the count table. I think my problem almost has to be with make.group, but I’m at a loss.
Below is the code to process a 3 sample run, but I have ~60 samples to do. I’m quite new to this, so if there’s an easier way, I’m happy to see it. Thanks for any advice! bob
fastq.info(fastq=Sed_15_S17_L001_R1_001.fastq)
trim.seqs(fasta=Sed_15_S17_L001_R1_001.fasta, qfile=Sed_15_S17_L001_R1_001.qual, oligos=oligos_16s.forward.txt, qwindowaverage=25, minlength=200, processors=16)
fastq.info(fastq=Sed_14_S16_L001_R1_001.fastq)
trim.seqs(fasta=Sed_14_S16_L001_R1_001.fasta, qfile=Sed_14_S16_L001_R1_001.qual, oligos=oligos_16s.forward.txt, qwindowaverage=25, minlength=200, processors=16)
fastq.info(fastq=Sed_13_S15_L001_R1_001.fastq)
trim.seqs(fasta=Sed_13_S15_L001_R1_001.fasta, qfile=Sed_13_S15_L001_R1_001.qual, oligos=oligos_16s.forward.txt, qwindowaverage=25, minlength=200, processors=16)
cat *.trim.fasta > combined.fasta
make.group(fasta=Sed_15_S17_L001_R1_001.fasta-Sed_14_S16_L001_R1_001.fasta-Sed_13_S15_L001_R1_001.fasta, groups=Sed_15_S17_L001_R1_001-Sed_14_S16_L001_R1_001-Sed_13_S15_L001_R1_001)
rename.file(input=Sed_15_S17_L001_R1_001.groups, new=combined.groups)
I CAN SEE THE DIFFERENT SAMPLE IDS WITH THE SEQUENCES IN THE GROUPS FILE
#M06789_65_000000000-KYGV4_1_1101_16721_1528 Sed_15_S17_L001_R1_001
#M06789_65_000000000-KYGV4_1_1101_16527_1357 Sed_14_S16_L001_R1_001
#M06789_65_000000000-KYGV4_1_1105_21607_10552 Sed_13_S15_L001_R1_001
#HERE’S WHERE I GET STUMPED NO MATTER WHAT I TRY
unique.seqs(fasta=combined.fasta, groups=combined.groups)