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.
I agree with Devon

I would do it in following ways:

1. Map fastq files with tophat2
2. Convert unmapped.bam file to fastq (bamTofatsq) and remap with tophat2, this time provide junctions ( with an option `-j` you got from first run, (if replicates then merge the junctions).
3. The unmapped.bam from this run can be converted to fastq.

I think that this is the fastq from which the reads you are looking for.