Question: Weird Outputs With Dynamictrim And Lengthsort On Custom Settings
gravatar for Biogeek
6.0 years ago by
Biogeek380 wrote:

Hi guys,

I am using Illumnia Hiseq sequence reads 100bp paired end raw data.I have been toying with data on Dynamictrim and length sort for some time.

When I want to use the settings q=25 (-h 25) and length sort ( -l 50). My data is trimmed first of all by dynamic trim and looks fine on fastQC,but when I carry out the second part (length sort) and put my .trimmed.paired 1 and .trimmed.paired 2 files through FastQC after length sort it says the quality is very low ( around 12-13) and in the histogram like graph of quality per reads all of the reads are down in the red. I have used the recent version (2.2) and also tried older versions just to ensure a bug isn't present.

When I use default settings … p=0.05 and Lengthsort ( -l 25) my results are actually quite good.

Now my problem is…although the data I get on default settings is probably good to use I would like it a little more stringent. I was advised to use a phred score of 25 as for my dataset, Q=20 is not stringent enough and Q=30 is too stringent? I was also advised as my raw reads are 100bp i should be looking at cutting the reads to a length of 50bp ( anything >50-100 bp is a good data input). This is coming from a bioinformatician, is there a good paper which explains why I should be doing this as I am still quite unclear?

Can I also just ask, using default settings is this fine or should I try and go with the custom settings.I am using the data for De novo transcriptome assemblage.

Many thanks.

qc • 1.5k views
ADD COMMENTlink written 6.0 years ago by Biogeek380
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1161 users visited in the last hour