Hi,
I'm hoping that this is a simple question, but I haven't found a tool to do specifically what I'm after yet.
I have illumina 2x150 PE reads. I'm using Trim-galore, which is a wrapper for Cutadapt to do adapter trimming as I have a lot of 3' adapter read-through. After this step, I'm left with mate-paired variable length PE reads. I then want to trim the first 5 reads which I can do with fastx toolkit.
My issue is that I then need to trim the last 5 reads. I can't use fastx toolkit since the fixed trim option is 'trim after n bases'. Given that each read will be different lengths after adapter read through at the 5'end, I can't use this option.
Can anyone suggest a way to do this please?
Thanks
I'm hoping that this is a simple question, but I haven't found a tool to do specifically what I'm after yet.
I have illumina 2x150 PE reads. I'm using Trim-galore, which is a wrapper for Cutadapt to do adapter trimming as I have a lot of 3' adapter read-through. After this step, I'm left with mate-paired variable length PE reads. I then want to trim the first 5 reads which I can do with fastx toolkit.
My issue is that I then need to trim the last 5 reads. I can't use fastx toolkit since the fixed trim option is 'trim after n bases'. Given that each read will be different lengths after adapter read through at the 5'end, I can't use this option.
Can anyone suggest a way to do this please?
Thanks
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