mothur

Trim.Seqs (Output blank)


#1

Hello friends,

I need help, I have a file Fasta with all samples and I also have an Oligos file, I need to know how to create the file .groups, so I can do the SOP analysis. I used the trim.seqs command, but the groups is left blank. What I’m doing wrong? There is another command?

Here are the commands I used:

trim.seqs(fasta=samples.fasta, oligos=samples.oligos)

Another information: My oligo file contains (separated by tab):

barcode. CCTGACACACAC Control_1
barcode CAGCGTTTAGCC Control_2
barcode GGTATGGCTACT Control_3
barcode ACAATGTCACAG Control_4
barcode GCCATAGTGTGT Control_5
barcode GGTCCCGAAATT Control_6
barcode TCTGCGAGTCTG Control_7
barcode ATGTAGGCTTAG Control_8
barcode GGCCAGTTCCTA Treatment_1
barcode GATGTTCGCTAG Treatment_2
barcode CTATCTCCTGTC Treatment_3
barcode ACTCACAGGAAT Treatment_4
barcode ATGATGAGCCTC Treatment_5
barcode GTCGACAGAGGA Treatment_6
barcode TGTCGCAAATAG Treatment_7
barcode CATCCCTCTACT Treatment_8

Thanks.


#2

what does the output in the scrap file look like? can you post a few examples of what the lines that start with “>” looks like?


#3

Pscloss, good morning.

I’m sorry, it was starting the wrong way. It worked out right now.

Thank you so much for answering me.

Have nice day.


closed #4

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