We will be offering mothur and R workshops throughout 2019. Learn more.
The list.seqs command will write out the names of the sequences found within a fasta, name, group, or align.report file. This could be useful for using the get.seqs and remove.seqs commands as well as to generate a group file. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.
At least one of the following options must be used. Each of these options will generate a file ending in accnos that contains a single column containing the list of the sequences contained in the input file.
The fasta option is used as presented in the following command:
mothur > list.seqs(fasta=esophagus.fasta)
The resulting esophagus.accnos file looks something like:
59_10_1 59_10_10 59_10_11 59_10_13 59_10_15 59_10_16 59_10_17 ...
The name option is used as presented in the following command (be sure to run unique.seqs on esophagus.fasta first):
mothur > list.seqs(name=esophagus.names)
The group option is used as presented in the following command:
mothur > list.seqs(group=esophagus.groups)
The alignreport option is used as presented in the following command:
mothur > list.seqs(alignreport=esophagus.align.report)