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Old 06-27-2016, 09:04 AM   #127
xuguorong
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Location: US

Join Date: Feb 2010
Posts: 27
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Hi Felix,

Thank you so much for your new release!
The new features definitely can remove all Ns from the reads! Awesome!

For the question 1, I want to try run cutadapt three times to keep the longer reads.
1: cutadapt -a adapter -q 10 -m 17 --trim-n -o $inputFile".trim.3.fastq" $inputFile".fastq"
2: cutadapt -g adapter -q 10 -m 17 --trim-n -o $inputFile".trim.5.fastq" $inputFile".fastq"
3: cat $inputFile".trim.3.fastq" $inputFile".trim.5.fastq" > $inputFile".trim.fastq"
4: cutadapt -b adapter -q 10 -m 17 --trim-n -o $inputFile".trim.final.fastq" $inputFile".trim.fastq"
5: then keep only one read and delete other one read with the same fastq ID.

The reason why I need to run 3 times is the first run cutadapt will trim the 3' adapter string, then the second run cutadapt will trim the 5' adapter string. After these two runs, some reads in $inputFile".trim.3.fastq" may still have 5' adapter string and some reads in $inputFile".trim.5.fastq" may have 3' adapter string. After I merged these two resulting files, then I run the third run cutadapt to cut either 3' and 5' adapter strings. Since I merged two fastq files and it will have some identical reads, I then scan the $inputFile".trim.final.fastq" to keep only one read and delete the other one with the same fastq ID.

Do you have any suggestions about this solution?

Thanks!
Guorong
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