anchored adapters from file

[GoogleCodeExporter]

I am trying to use the --no-indels option but my primers (anchored) are 
provided as a fasta file, and it is not running. It keep coming back with an 
error 
"cutadapt: error: Not allowing indels is currently supported only for anchored 
5' adapters."
the adapter seqs in my file does start with ^ .
Am I doing something wrong or is this not supported yet?
Thanks.

sherry

Original issue reported on code.google.com by san...@swiftbiosci.com on 6 Nov 2014 at 1:56

[GoogleCodeExporter]

That's a bug: The ^ character in the FASTA file is not recognized (it is 
currently recognized on the command line only). I'll see if I can fix that 
within the next days.

Original comment by marcel.m...@tu-dortmund.de on 6 Nov 2014 at 5:12

[GoogleCodeExporter]

Thank you. So I assume no anchored-adapter trimming from fasta file yet? you 
said you may enable it. Thanks for that. Will you consider anchored adapter 
trimming from both 5 & 3' using adapter fasta file. thanks again. 
Best!

Original comment by san...@swiftbiosci.com on 6 Nov 2014 at 5:46

[GoogleCodeExporter]

Sure! I will fix both at the same time.

Original comment by marcel.m...@tu-dortmund.de on 6 Nov 2014 at 6:49

[GoogleCodeExporter]

Hi, I’ve just committed a fix for the problem. Do you know how to get a new 
cutadapt version from Github?

Original comment by marcel.m...@tu-dortmund.de on 6 Nov 2014 at 7:10

[GoogleCodeExporter]

thanks a lot,.I can try,.should I just clone it again?

Original comment by san...@swiftbiosci.com on 6 Nov 2014 at 7:40

[GoogleCodeExporter]

it seems I got the new version: cutadapt version 1.7dev; but may be I am not 
putting --no-indels at the correct position & I still keep getting the same 
error.
commandline is below:
cutadapt -g file:primersF5anchored.fa --no-indels -a file:primersRev.fa -o 
s17R2_gForaRevnoindel.fq star.fastq

Original comment by san...@swiftbiosci.com on 6 Nov 2014 at 8:20

[GoogleCodeExporter]

You can update to the newest version by running "git pull", you don't have to 
clone again.

Which version did you run before? If that was also 1.7dev, are you now sure you 
are actually running the newest version?

Also, all adapters in primersF5anchored.fa need to be anchored (they need to 
have ^ in front), and all adapters in primersRev.fa need to be anchored (they 
need to have $ in the end). If you still cannot find the problem, could you 
send me the two files with adapters (via e-mail)?

Original comment by marcel.m...@tu-dortmund.de on 6 Nov 2014 at 9:49

[GoogleCodeExporter]

Thanks, actually the version before was 1.4, I got the 1.7dev after your
message.
I am able to do anchored trimming from file, thanks a lot for your prompt
attention.
but it doesn't run with --no-indels.
Best

Original comment by san...@swiftbiosci.com on 6 Nov 2014 at 10:02

[GoogleCodeExporter]

I'll check that tomorrow, maybe I've overlooked something.

Original comment by marcel.m...@tu-dortmund.de on 6 Nov 2014 at 10:06

[GoogleCodeExporter]

You said "but it doesn't run with --no-indels.", and I have re-checked that 
now. I cannot reproduce that: It works on my test data here. If you still have 
the problem and want me to fix it, I will need the exact command line that you 
are using and also the FASTA files with the adapter sequences.

Original comment by marcel.m...@tu-dortmund.de on 7 Nov 2014 at 11:26

[GoogleCodeExporter]

I used the same command line I wrote above, that's what I was asking i.e. if 
--no-indel goes after each anchored file or just once in the front. Can you 
please share your command line with anchored adapter file with noindels option. 
Thanks

Original comment by san...@swiftbiosci.com on 7 Nov 2014 at 11:33

[GoogleCodeExporter]

The position of the --no-indels option does not matter; you can put it anywhere.

If you still get the message: Are *all* adapters in *both* files anchored?

Original comment by marcel.m...@tu-dortmund.de on 7 Nov 2014 at 3:30

[GoogleCodeExporter]

I’m assuming the problem has been solved.

Original comment by marcel.m...@tu-dortmund.de on 13 Nov 2014 at 9:58

• Changed state: Fixed

[GoogleCodeExporter]

Yes it is,..sorry for the delay in getting back, and thanks a lot for your
help and this great tool. best!

Original comment by san...@swiftbiosci.com on 13 Nov 2014 at 9:56

[GoogleCodeExporter]

No problem, and great to hear it’s fixed!

Original comment by marcel.m...@tu-dortmund.de on 14 Nov 2014 at 8:31

[GoogleCodeExporter]

Hi again, I was wondering if you can also enable 3' anchored adapter/primer
trimming from a file of adapter/primer sequences. I tried with a $ at the
end of my sequence and it didn't work. Thanks a lot.
Best

Original comment by san...@swiftbiosci.com on 26 Jan 2015 at 7:48

[GoogleCodeExporter]

Strange, this should already work. To make sure: Which cutadapt version are you 
using, how does your command line look like and what are the contents of the 
adapter file?

Original comment by marcel.m...@tu-dortmund.de on 27 Jan 2015 at 11:26

[GoogleCodeExporter]

you are right, it was a formatting issue. It works great. Thanks again.
Best!

Original comment by san...@swiftbiosci.com on 27 Jan 2015 at 2:44

[GoogleCodeExporter]

Cool, happy to hear that!

Original comment by marcel.m...@tu-dortmund.de on 27 Jan 2015 at 3:14