Generate group file from count file (make.contigs)

Commands in mothur
1

Hi,

With the latest v1.47, make.contigs() will generate count files instead of group files. That’s great ! BUT for our project and data sets, we will still need the group file.

Just wondering is there an easy way to generate the group file from the count file ?

Thank you

2

You can run the following:

mothur > deunique.seqs(fasta=fastaFileFromMakeContigs, count=countFileFromMakeContigs) - creates a fasta and group file

3

Thanks ! I tried that and it worked. But it seemed like Mothur appended “_1” to the sequence name (which I had to run a sed command to remove them), is there a setting to turn it off ?

4

The “_x” is added to distinguish identical reads from different groups. Consider this example:

Representative_Sequence total group1 group2 group3
seq1 3 2 0 1

seq1 represents 3 reads so deunique.seqs will add 3 reads to the fasta and 3 reads to the group file.

seq1_1 group1
seq1_2 group1
seq1_3 group3

Since your sequences are unique the “_1” is not necessary and can be removed.

5

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.