Dear all,

I have pair-end RNA-seq data (Illumina) from parasite and I would like to do De-Novo assembly by TRINITY. I have reference genome of my host organism so I can map my data to host and remove from fastq contaminations.

My plan is:

1. Map with bwa/bowtie/novoaling my pair-end FASTQ files to a host reference genome
2. Remove hits from fastq files (cleaning contaminations)
3. For the rest of FASTQ files use TRINITY for De-Novo transcript assembly

My question is:

May I use aligners (bwa etc.) and align raw fastq files to host DNA and then remove contaminants from fastq files? Question is because my data are from RNA-seq project NOT DNA.

How can I remove the sequences from raw fastq files that align to host DNA (cleaning process)?

Or if you have any other advice how to prepare data to TRINITY pipeline I will appreciate it.

Thank you so much for any comment and sharing your experience.
If you would like a Galaxy solution, this filters by ID: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id / https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id

This filters using a SAM/BAM mapping file: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping / https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs / https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping