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Old 06-09-2011, 05:59 AM   #16
Himalaya
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Location: uk

Join Date: Jun 2010
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Quote:
Originally Posted by Jose Blanca View Post
Sorry, I have not explained myself well enough.
clean_reads uses two different algorithms for quality trimming. One for long reads (lucy) and a different one for short reads. If you're cleaning long reads, the parameters aplicable are the lucy parameters: lucy_error, lucy_window and lucy_bracket. These are the parameters that you should tweak to modify the cleaning behaviour when dealing with 454 and sanger reads.

For illumina and solid we didin't manage to use lucy so we implemented a sliding window trimming function. Its parameters are qual_window, qual_threshold, and only_3_end. That's why these parameters can only be used with short reads.
Hi Jose
I am going with your explainations. I issued the followed command:
clean_reads -i Pair01_fastq_format.fastq -o ./clean_reads/output_q20_len_50 -p 454 -f fastq -g fastq -min_length 20 --lucy_error 0.025,0.02 --lucy_bracket 10,0.02 --lucy_window 1,0.02

It seems to work fine but no output. The clean_reads.error explains that the input file "Pair01_fastq_format.fastq" is not found. The file is in the same directory from where i issued the command and it says "no such file or directory".
Am i wrong in the command itself?
I really appreciate your help. Thnx
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