Trimmoatic: Command for cutting bases from the start and end of the read

[newfie]

Hi everyone,

I am working with small non coding RNA data. I removed my adapter sequences from my data. However, there are random miRS of 4 bases attached to both the start and end of the reads. Hence, i wanted to remove 4 bases both from the start and end of the read. I used the command HEADCROP 4 to remove bases from the start of the read. However, i am not quite sure which command to use, to remove bases from the end of the read. the CROP command doesn't cut the bases at the end of the read, however it cuts the read to specified length by cutting the bases from the end of the read. The TRAILING command could be used, but i am not quite sure what would be threshold quality value that could trim the 4 random mirs. Because i need all the 4 bases to be uniformly trimmed across all the reads. Any thoughts? Opinion? Suggestions? I know cutadapt could be used in this case. But since i have already used trimmomatic to cut adapters i want to use the same for trimming the 4 bases from the start and end of the read.

Thanks

[newfie]

^^^^ or in other words i am wondering if there is a TRAILCROP option in Trimmomatic

[mastal]

The problem with removing bases from the 3' end of the reads is that, even after adapter trimming, there may be some reads that had only a few bases of adapter sequence, so too short to be removed by trimmomatic, and you would be removing those instead of the miRS sequences.

As far as I know there isn't an option that does what you want in Trimmomatic, unless you start with reads all the same length without any adapter contamination.

[Zaag]

^^^^ or in other words i am wondering if there is a TRAILCROP option in Trimmomatic

CROP: Cut the read to a specified length

[mastal]

CROP: Cut the read to a specified length

Yes, but that won't help if your reads are all different lengths because you have removed variable lengths of adapters from the 3' ends.

[Zaag]

True, but you can leave the adapters on and just cut adapter + 4 bp

I know PrinSeq has this option:
-trim_right

Trim sequence at the 3'-end by trim_right positions

http://prinseq.sourceforge.net/manual.html

but I never used it.

Cheers.

[GenoMax]

@newfie: You could use the CROP command first followed by HEADCROP/trimming if you want to stick with trimmomatic. (If you want to remove an additional 4 bp from what was left after the trimming, then this won't work).

bbduk.sh will allow you to forcetrimright=n past a certain position.