Remove adaptor from 5' end in color-space data

[GoogleCodeExporter]

What steps will reproduce the problem?
1. The option -g does not work with color-space data. The script says "Using 
--anywhere or --front with color space reads is currently not supported  (if 
you think this may be useful, contact the author)."

What is the expected output? What do you see instead?
Trimmed reads for 'de novo' RNA-Seq

What version of the product are you using? On what operating system?
v1.0 on Rocks Viper

Please provide any additional information below.
I'm working with the same datase using the new ECC module that allows you to 
convert color-space into base-space data and from that I know there are 
adaptors in the 5' end in my reads that should be removed prior the 'de novo' 
assembly of my data. I detected these adaptors using your tool with the reads 
in base-space but now I'd like to do the same process with the data in 
color-space but I'd need to removed the adaptor in the 5' end. Any ideas about 
how to perform 5' adaptor removal in color-space data?

Thanks very much in advance.

Sheila

Original issue reported on code.google.com by szu...@gmail.com on 16 Apr 2012 at 3:44

[GoogleCodeExporter]

How exactly do the adapters appear in the read? Let’s say the adapter has ten 
bases. Is it possible that a read contains only the last few bases of the 
adapter? The -g parameter allows this, but I’m still not sure whether this is 
the correct behavior, even for base-space data. Or will it be the case that the 
always (or almost always) starts with a full adapter sequence? 

Could you send me a few reads that contain 5' adapters and also tell me the 
adapter sequence in base space?

Original comment by marcel.m...@tu-dortmund.de on 17 Apr 2012 at 7:52

• Added labels: Type-Enhancement
• Removed labels: Type-Defect

[GoogleCodeExporter]

I'll close this issue for now as I don't know how to implement the requested 
feature. Please comment if you have more information.

Original comment by marcel.m...@tu-dortmund.de on 12 May 2012 at 10:17

• Changed state: Invalid

[GoogleCodeExporter]

This has been implemented in the soon to be released cutadapt 1.1.

Original comment by marcel.m...@tu-dortmund.de on 17 Jun 2012 at 5:31