I am new to using mothur and in attempting to follow the MiSeq_SOP guide with my data on 18S rRNA v4 sequences I am stumped in the beginning. The guide assumes you want to make contigs from paired-end reads, but I would like to analyze my forward reads separately. How do I combine just my read 1 fastq files, retaining the sample name for all the sequences in each file of course, so that I can proceed with the following alignment and classification steps? I can't seem to find an explanation on how to do this anywhere.
Hey guys, I know this is over a year old but I found out something that can fix this. Currently we are using mothur to analyze our PacBio data which comes as a bam file. We then convert the bam to a fastq file and ran into the same issue mentioned above.
So lets say I have 5 samples after we convert to fastq called 101.fastq, 102.fastq, 103.fastq, 104.fastq and 105.fastq.
First go into mothur and run
fastq.info on all the samples (if using pacbio make sure to use the
Then run a command called make.groups(), for this example this command would look like;
This results in a file called mergegroups (you can easily rename this)
Then exit mothur (or run a system() command) and run
cat *fasta > combo.fasta
to combine your fasta files. Then go back into mothur and treat the mergegroups file and the combo.fasta file like the output you would get from a make.contigs() command.
Hope this helps!