The l in the "-l" is the lower case of L, not the upper case "I".
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xiaoleiusc
cutadapt for trimming reads to specific length
Hi I am trying to trim my fastq files where I have reads ranging from 20bp to 150bp as shown by fastqc result. I want to keep a definitive length of my reads to 120bp. So if any read is greater than 120 bp trim it to 120 and if any read is less than 120 then discard it. How can I do this using cutadapt?
I can use -m option to throw away reads less than 120 bp but I still get reads greater than 120 bp. How can I trim them to 120 bp.
This is the command I am using
cutadapt -m 120 -o file1.trimmed.fq -p file2.trimmed.fq file1.fq file2.fq
Also can trim galore do that?
Thanks
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xiaoleiusc
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Varun Gupta
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Varun Gupta
5 answers
Trimmomatic can achieve this one nice and easy. Just use the parameter CROP, which uses a number of bases you want to keep.
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biofalconch
I will try this. Thanks
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Varun Gupta
Hi Varun,
I do this in two separate steps. I first remove the adapters and run fastqc and then depending on the read quality of the new file, I trim them to required size using fastx_trimmer. The reason being that removal of adapter changes sequence quality on fastqc. So parameters for trimming change.
Best,
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Satyajeet Khare
-m is minimal length
-M is maximum length
per the manual:
-m LENGTH, --minimum-length=LENGTH Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Default: 0 -M LENGTH, --maximum-length=LENGTH Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Default: no limit
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datascientist28
I don't want to discard the reads which are longer than 120 bp but trim them to 120 bp. That is not what -M is doing
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Varun Gupta
oh my bad that's what I get for skimming the question
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datascientist28
-M option would discard reads longer than 120 bp. I want to trim it if they are longer than 120 to 120bp
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Varun Gupta
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If your goal is just to trim the reads, why do you want to use cutadapt ? You could use something like fastq_trimmer
This would also be pretty simple to do in python. For example, altering this script by adding an:
if len(line) >=120:you don't even need a script for that. You could do it with awk.
I was using cutadapt so thought this would be possible using it. I will look into fastq_trimmer. Thanks
Since no one has asked this I will. Why do you want to do this? Unless the reads have really poor Q-scores (< Q10) or show presence of adapters, there should be little reason to trim them. Far too many people take "failures" of FastQC modules seriously.
Hi genomax2, The reads are fine as far as quality scores are concerned. The reason I want to do this is I am using rMATS downstream which as of now requires fixed length of the reads.
Hi, Varun,
I asked similar questions in the rMATS forum. I have pair-end fastq reads with a length of 151 bp. After adaptor trimming, the length is not uniform for all reads, the developer told me that I can still use "--variable-read-length --readLength 151" arguments in the command line. I tried and this works for me.
Xiao