OTN adaptors, same barcodes on F and R primers, outputs and revcomp sequences

[l-yampolsky]

Thank you, this is exactly the tool I've been looking for. It perfectly matches my trimming/demultiplexing needs. I have several questions.

1. Do I need to supply minibar with just my barcode sequences or also ONT adapter sequences? (I used pretty much the same ligation kit you use in the Gigascience paper, only the next version). It appears that your example files only contain the primers with barcodes. What happens to the adapters? Are they removed automatically as minibar removes barcodes?
2. I used much shorted (Illumina, 6nt) barcodes than those used in your test files. Should not be a problem, right (also shorter amplicones)?
3. answered by trial
4. -S outputs sequence record in fasta or fastq format of input (default output) -- does this mean that whatever format is input, the same format will be in the output? No way to have fastq as input but save fasta as the output? Would have been useful.
5. I did not understand why it is necessary to provide revcomp index and primer seq's in Index Combination file. Is that file needed? (apparently not)

Thank you so much in advance!

[l-yampolsky]

and to bother you more, what does it mean when Minibar saves files that look like this:
~/Desktop/18S/testMinibar$ ls -l
-rwxrwxrwx 1 ly staff 5.9M Nov 28 12:27 _475.fastq*
-rw-r--r--@ 1 ly staff 168B Dec 1 20:50 demuxWaterSoil.txt
-rw-r--r-- 1 ly staff 2.0M Dec 1 21:17 sample_Soil.fastq
-rw-r--r-- 1 ly staff 279K Dec 1 21:17 sample_Soil_Water_Soil_Water.fastq
-rw-r--r-- 1 ly staff 2.5M Dec 1 21:17 sample_Water.fastq
-rw-r--r-- 1 ly staff 1.3K Dec 1 21:17 sample_Water_Water.fastq
-rw-r--r-- 1 ly staff 507K Dec 1 21:17 sample_unk.fastq

I would imagine that sample_Water_Water.fastq are chimeric reads where on both ends there is a read from my "Water" sample. Not sure why, but the reads in this file are not longer than usual. But what is sample_Soil_Water_Soil_Water.fastq?

[HAHasani]

Hi,
I'm also wondering about the repeated id in the output (in your example water_water)?

[thecorz]

I am getting the same problem with the output file names. I'll open a separate issue for it #7