Question: mate pair trimming ?
1
gravatar for Picasa
4.8 years ago by
Picasa590
Picasa590 wrote:

Prior to an assembly, I would like to trim out adaptor sequences from mate pair library.

I use usally Trimmomatic, but it doesn't suit for mate pair because of orientation right ? Do you have any recommandation for mate pair trimming ?

mate pair • 2.3k views
ADD COMMENTlink modified 4.8 years ago by Chris Fields2.2k • written 4.8 years ago by Picasa590
2

You can try Cutadapt. More information can be found: Trimming Adapters

ADD REPLYlink written 4.8 years ago by DVA550
2
gravatar for Antonio R. Franco
4.8 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.6k wrote:

Take a look to BBDuk. There is plenty of information about it HERE

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Antonio R. Franco4.6k
1
gravatar for Shicheng Guo
4.8 years ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

You can try Trim_galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/:

Single end

trim_galore $phred --fastqc --illumina --clip_R1 3 --clip_R2 3 $read[0] --output_dir ../fastq_trim

Pair-end

trim_galore $phred --fastqc --illumina --paired --clip_R1 3 --clip_R2 3 --three_prime_clip_R1 3 --three_prime_clip_R2 3 $read[0] $read[1] --output_dir ../
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Shicheng Guo8.5k
1
gravatar for Chris Fields
4.8 years ago by
Chris Fields2.2k
University of Illinois Urbana-Champaign
Chris Fields2.2k wrote:

If you are removing the Nextera internal adapter for mate-pair libraries, you should use NxTrim:

https://github.com/sequencing/NxTrim

This will both trim the internal adapter and categorize the reads into groups: true mate-pairs, single-end, paired-end, and unknown (no adapter found, so likely a mix of true mates and paired-end). Note that the tool will revcomp the output by default to make them innies, which is NOT what most assemblers want. You can stifle this to keep the outie orientation by using the --norc option.

Otherwise, the above choices will work for other standard adapter sequences.

ADD COMMENTlink written 4.8 years ago by Chris Fields2.2k
1

I' want to try this soft with a mate pair library (insert length of 3000). So what is the differentce between theyr true mate and their paired end ? is the paired end still have an insert length of 3000 ?.

Does is trim sequencign adaptor too ? (like P1 etc.)

ADD REPLYlink written 4.8 years ago by Picasa590
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