Hi,
I would be most grateful for your help please. I am trying to generate the required files for downstream analyses with PICRUST2. I am referencing your github code on https://github.com/SchlossLab/Sze_SCFACRC_mBio_2019/blob/master/code/asv.sh
I have ran the mothur > make.shared(count = inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table , label = ASV, outputdir=asv/)
Setting output directory to: asv/
Output File Names:
asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.shared
asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.list
I am stuck at the rename.seqs section. I don’t seem to have any files with the suffix pick.pick.pick.map
[sample from Marc Sze code: map=$WORKDIR/crc.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.pick.map]
The only files that I have is the *.trim.contigs.good.unique.good.filter.unique.precluster.{name of sample}.map
The files that have with the .trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick. is as follows:
./asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.shared
./asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.list
./inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table
I am using mothur v.1.44.1
Could you please advise on how I can generate the map file please?
Thank you