Question: LEADING and TRAILING in TRIMMOMATIC
2
gravatar for grant.hovhannisyan
11 months ago by
grant.hovhannisyan1.5k wrote:

Hi Biostars,

I have been using trimmomatic for quite some time, but realized that I don't get something. So one can use LEADING and TRAILING options to remove bases from the beginning and end of the read, respectively. From manual: LEADING Remove low quality bases from the beginning. As long as a base has a value below this threshold the base is removed and the next base will be investigated.

My question is: "From the beginning" means from the beginning until the end of the read? If yes, then what is the meaning of having TRAILING option if the whole read is scanned? Otherwise, until which base does trimmomatic scan by LEADING option?

Cheers,

rna-seq trimmomatic • 1.4k views
ADD COMMENTlink modified 11 months ago by YaGalbi1.4k • written 11 months ago by grant.hovhannisyan1.5k
2
gravatar for YaGalbi
11 months ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

According to the documentation both both options take the argument "quality":

LEADING:quality

leading: Cut bases off the start of a read, if below a threshold quality

quality: Specifies the minimum quality required to keep a base. Remove low quality or N bases.

Also from the manual: LEADING - Remove low quality bases from the beginning. As long as a base has a value below this threshold the base is removed and the next base will be investigated.

"LEADING 3" would delete all bases below a quality threshold of 3 or that are N, beginning at the first base and continuing until the first base that is at least a quality of 3 and is not N

AAAGGGTTT 012345678 - Leading 3 would cause the deletion of AAA

AAANNNTTT 012345678 - Leading 3 would cause the deletion of AAANNN

AAAGGGTTT 123456789 - Leading 3 would cause the deletion of AA

Same happens with trailing but from the other end

ADD COMMENTlink modified 11 months ago • written 11 months ago by YaGalbi1.4k

Thanks, now it make sense to me.

ADD REPLYlink modified 11 months ago • written 11 months ago by grant.hovhannisyan1.5k
1
gravatar for Expe
11 months ago by
Expe10
Expe10 wrote:

I think that with the leading option you only remove a few nucleotides at the beginning of the reads and keep the rest. The trailing option does the opposite: it removes the nucleotides at the end of the read. This site and this site explain why nucleotides should be removed from the beginning and from the end of the reads (you keep the ones in the middle then).

ADD COMMENTlink written 11 months ago by Expe10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1874 users visited in the last hour