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alexstaj / cutadapt

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output additional info about the cut adapters #3

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
This suggestion was made by "hash" in the seqanswers forum:

"Also, it would be useful to track which sequence was trimmed as adapter and 
where in the original sequence it was trimmed from in terms of location. Maybe 
an optional dump .fastq file would help for this which would contain the 
trimmed adapter sequence and additional information as to where in the original 
sequence it was found and how many mismatches were allowed (e.g. if a sequence 
is 36bp and adapter is found at 1 to 15bp with 0 mismatches, then maybe you 
could append this information to the '+' line in the fastq file as 1_15_0; the 
rest of the fields for a fastq sequence entry i.e. '@' would be the same)."

Original issue reported on code.google.com by marcel.m...@tu-dortmund.de on 2 Dec 2010 at 1:30

GoogleCodeExporter commented 9 years ago 
I suggest a table list of read names and mapping info.
Read sequence is optional to write to the list.

I don't think  it is necessary to keep FASTQ format for this popurse.

Original comment by galaxy...@gmail.com on 29 Apr 2012 at 2:09

GoogleCodeExporter commented 9 years ago 
This is now in cutadapt 1.2. Just use the '--info-file' option.

Original comment by marcel.m...@tu-dortmund.de on 4 Dec 2012 at 10:22