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.
I have a similar question. Any luck in finding a solution?
Can't you just skip the
make.contigs()
? Try preparing thestability files
with just R1.You may also have to hack your way and change your file names to the same pattern Mothur uses after the
make.contigs()
step.But
make.contigs()
is the step where a quality information filter is applied as fastq files are converted to fasta files. If you skipmake.contigs
how do you get a fasta file? I tried making a .files table with only the forward fastq listed but wasn't able to get it to work. If you did, could you please share an example of the format?Thanks! I am having this same problem trying to re-analyze some old public datasets (sequenced before paired end was a thing.)
Here is the description of the .files file format. You'll notice every format option includes a forward and reverse read: https://www.mothur.org/wiki/Make.contigs#file
Hello guys, I am new to Galaxy and I have the same problem. I tried what is said above. fastaq.info created 5 files but all were empty (0bytes). So I tried the following (all using galaxy): 1) Concatenate fastaq files (to create one single fastaq file of my 7 fasta qfiles) 2) converted my concatenate fastaq file to fasta 3) created a group from the concatenate fasta file. 4) then I ran unique.seq and I used the group file "group" and the concatenate fasta file as the "fasta" file. It failed. Checking the gorup file, I believe I lost the information related to which sequences belong to which samples...could it be the reason? how to fix that? In brief, how to run galaxy using singe reads? easy step by step for a beginner like me. Unfortunately, my data quality are poor and hence I must trim long stretches (100 bp out of 300bp), this resulted that the forward and reverse reads to not form contigs. Thank you very much guys..it is my first time and I feel totally lost... Cheers