Trim last 'n' reads from end of variable length PE reads

[swNGS]

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

[JackieBadger]

Use Trimmomatic

[swNGS]

Hi JackieBadger

Thank you for your suggestion, I did look into Trimmomatic. As far as can see the options are as follows:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
LEADING: Cut bases off the start of a read, if below a threshold quality
TRAILING: Cut bases off the end of a read, if below a threshold quality
CROP: Cut the read to a specified length
HEADCROP: Cut the specified number of bases from the start of the read
MINLEN: Drop the read if it is below a specified length
TOPHRED33: Convert quality scores to Phred-33
TOPHRED64: Convert quality scores to Phred-64

My interpretation is that Trimmomatic wont let me trim a fixed amount regardless of quality from the end of a read.
If all my reads were the same length this would be easy as I could use fastx_trimmer and invoke the -l switch (meaning number of bases from which to trim). I need to ditch the adapter read-through before trimming the 'real' sequence, hence the variable sized reads.

As far as I can see the only 3' end trimming option offered by Trimmomatic is based on quality thresholds rather than an absolute number regardless of quality.

I'm sure there must be a simple answer to this, but I've yet to spot it

[swNGS]

seqtk looks promising:

The following apparently trims 5 bases from the left (5' end) and 10 bases from the right (3' end):

seqtk trimfq -b 5 -e 10 in.fa > out.fa

Adapted as:

seqtk trimfq -e 5 in.fa > out.fa

should do the trick

[JackieBadger]

Ahhh ok...sorry about that.
You're right.
For this kind of trimming I use Galaxy.
You can either trim Fastq files... or convert to tabular format and from txt.
For larger files it is better to install a local instance. It's worth it as Galaxy provides a great way to edit and convert files

https://main.g2.bx.psu.edu/