Question: Trimming read length & quality in a FASTQ file
0
gravatar for ChIP
4.0 years ago by
ChIP490
Netherlands
ChIP490 wrote:

Hi all,

I was having a different computational problem, I had to compare a single end RNA-seq to paired end RNA seq. So my approach was to take the forward strand reads from the paired end sample and trim the read length and quality score of this fastq file and then map it using BWA, followed by regular stuff of estimating RPKM.

But how can I trim the read length and quality score?

any one liners in perl or awk to do this or is their something in picard tools?

Please share your experience and knowledge.

 

Thank you

rna-seq next-gen • 4.7k views
ADD COMMENTlink modified 4.0 years ago by gufernandez1010 • written 4.0 years ago by ChIP490
2

https://github.com/lh3/seqtk

http://www.usadellab.org/cms/?page=trimmomatic

In case, both of your paired end reads are in the same file first separate them and then trim the forward reads.

Suggestion: If your goal is to compare these two set of files for the end results (RPKM) in your case I don't think there is any point in just considering forward reads. You can compare a fragment library with a paired-end library and compare their complexities, contamination etc. And please use Splice aware aligner like TopHat or STAR if you want to count the reads spanning exons. 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Ashutosh Pandey11k

If the pairs are in separate files, you could just work on each file and substr() on awk when NR%2==0, no?

ADD REPLYlink written 4.0 years ago by RamRS21k
1
gravatar for gufernandez10
4.0 years ago by
Chile
gufernandez1010 wrote:

Hi i'm doing something similar, im using to trim reads features with cutadapt , is a good option and easy to use. 

http://cutadapt.readthedocs.org/en/latest/guide.html

ADD COMMENTlink written 4.0 years ago by gufernandez1010
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