Tool:tool to reorder mate reads after preprocessing

Question

[Anil Kesarwani]

Hi,

I removed adapter sequences individually from mate 1/ and 2/ fastq files using fastx tool. Following that I also removed the reads which are mapping to rRNA and the plasmid genome present in fastq.

After these processing steps, the mate1 and mate 2 reads in two files, as obvious, are not in order. Is there any tool to arrange the reads in a proper order in the two files, and remove those reads whose corresponding mate was filtered out during processing steps. I will highly appreciate if someone can help me out.

[Istvan Albert]

The right solution is to use a trimming tool that handles pairs correctly, like trimmomatic

[Ashutosh Pandey]

Istvan is right. You will spend more time in figuring out how to put reads in proper order than reprocessing the original fastq files from scratch using trimmomatic. It is a jave based tool and can work with compressed (.gz) fastq files.

[Anil Kesarwani]

Thanks for your suggestion

[Anil Kesarwani]

Trimmomatic removes adapter sequences and keeps the mate pairs in the same order. However, following this step, I am separating reads mapped and unmapped to the rRNA sequences (reference) in new fastq files using bowtie2. I realized that in the resulting fastq files, the order of mate pairs are lost. Is there any option to keep the order. The read pairs which are NOT mapped to rRNA will be aligned against genome (reference) in the next step.

Answer 1

[Ashutosh Pandey]

Nothing can beat this simple solution from Heng Li here.