As GenoMax says, trimming to Q30 is not beneficial before merging reads. BBMerge has some internal quality-trimming options, so it can try to merge, then quality-trim if it is unsuccessful, then try to merge again, etc. That can slightly increase the merge rate. But typically I just use the whole untrimmed reads as input. The longer the input reads are, the less likely it is for BBMerge to make an accidental incorrect merge, and it does take quality scores into account, so I do not recommend quality-trimming prior to BBMerge. Adapter-trimming is fine though.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Merge pairs before normalisation?
Hello, I'm building a pipeline for metagenomics.
I follow the bb tools user guide and do:
- normalization with bbnorm
- error correction with tedpole
- merge (with extension) with bbmerge
I want to increase the merging to get a better assembly.
I suspect that many reads, which could be merge are thrown away during the normalisation.
Wouldn't it be better to do merging (without extension) first than taking primarily the merged reads, normalize, error-correct and merge with extension?
What is the best way of normalising paired end and merged pairs or singletons in bbnorm?
For now I do two rounds of bbnorm and supply the other reads via the `extra` parameter, is there a better way to do?
Comment
-
Hi,
I have the shotgun data. Paired-end reads 100bp each end. I want to do MetaPhlAn2 next to know the general taxonomy profile.
So I am considering to merge them before the MetaPhlAn2. However, I do not know I need to run bbmap first to do quality control, OR to run bbmerge first to merge the sequence. Any suggestions?
Thanks in advance
Comment
-
@chloe - It's normally simplest and most effective to do QC first on the raw data, then anything else (such as merging) later.
@silask - they way you are doing it is currently the most effective way. It's a little bit annoying to have to run BBNorm twice, but that's the only way to process both paired and unpaired reads.
Comment
-
Hi, Brian,
Thanks for the reply. However, I have tried the QC. I used
bbduk.sh in=R1.fastq.gz out=filter_R1.fq maq=30
bbduk.sh in=R2.fastq.gz out=filter_R2.fq maq=30
(no reads in R1R2 will be trimmed)
bbduk.sh in=R1.fastq.gz out=clean_R1.fq trimq=30
bbduk.sh in=R2.fastq.gz out=clean_R2.fq trimq=30
(it will trim 50% of reverse reads, but no forward reads)
bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1_001.fq out2=R2.fq outm=fail.fq bhist=hist_base.txt qhist=hist_q.txt aqhist=hist_aq.txt bqhist=hist_bq.txt ecco=t
(Also no reads will be trimmed)
But when I run the code BBmerge, only 32.268% of the reads can be joined.
Do you have any suggestions?
Thanks in advance.
Comment
-
@chloe1005: It is possible that only 32% of your reads have inserts of a size that the reads can merge.
`trimq=30` is too severe a bar for trimming. If you have a reference genome then not doing any trimming for quality works fine. If you are doing any de novo work then you may want to trim at Q20 or Q25.
Comment
-
Hi,
I am still confusing about the difference between the quality trimming and quality filtering. What is the difference between them?
May also know how to get the reference genome? Since I also see the first threads in this post.
Looking forward to getting the answer.
Comment
-
RQCFilter Norm and EC
Hi Brian,
I am trying to trim and filter my data with RQCFilter but I cannot find an option for normalisation and error correction. Are there any parameters in this package? Also there is a parameter called -merge. Does it do merging? Should I set it to false and try normalising and error correcting first?
Comment
-
Source: https://jgi.doe.gov/data-and-tools/b...preprocessing/
"These steps replicate the QA protocol implemented at JGI for Illumina reads. There is a program “RQCFilter” which implements them as a pipeline, but that is not publically available because it has numerous hard-coded paths to reference datasets of contaminants."
It is in the bbtools files.
Nevermind! 1) Is it a good plan to normalise and error correct first BEFORE merging? 2) Do I need to follow a different approach at trimming and filtering short vs long mate pair reads (Nextera)?Last edited by kokyriakidis; 07-08-2018, 12:15 PM.
Comment
-
Since notes on the page you linked say this:
There is a program “RQCFilter” which implements them as a pipeline, but that is not publically available because it has numerous hard-coded paths to reference datasets of contaminants.
In general @Brian has recommended merging reads before doing any additional manipulations.
Comment
-
Originally posted by GenoMax View PostSince notes on the page you linked say this:
You should follow the steps that are denoted to replicate that functionality on the linked page.
In general @Brian has recommended merging reads before doing any additional manipulations.
Comment
Latest Articles
Collapse
-
by seqadmin
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...-
Channel: Articles
09-09-2024, 10:59 AM -
-
by seqadmin
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...-
Channel: Articles
08-27-2024, 04:44 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 06:25 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
Today, 06:25 AM
|
||
Started by seqadmin, Yesterday, 01:02 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 01:02 PM
|
||
Started by seqadmin, 09-18-2024, 06:39 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-18-2024, 06:39 AM
|
||
Started by seqadmin, 09-11-2024, 02:44 PM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-11-2024, 02:44 PM
|
Comment