Align unmapped reads to virus genomes

[SuzuBell]

Hello,

I am trying to determine how much of the unmapped reads from a transcriptome study align to viruses. My procedure so far has been to:

1) Download the complete genome of a virus in FASTA format. Here is one example I used (https://www.ncbi.nlm.nih.gov/nuccore...1?report=fasta)

2) Take my RNA-seq fastq file and run GSNAP to align it to the reference of interest (honeybee genome).

3) Now I would like to use the .nomapping file that is output from GSNAP and see how many of its reads map to the virus FASTA file of interest.

The .nomapping file is in the below format:

HISEQ:596:HKK7FBCXX:2:2216:18465:100529 272 GroupUn3757 1317 3 6S94M * 0 0 AATGCAAAAAAATAATAAACAATGATTTTAATTTCAACGACGTAAATTTCCGAATTTTGGGTGCGAATGTAGATGACTTAATGAGAAACACTCGTTGCGG IHHC?HHHIIIIIIIIIIIIIIIHFEHG<IHHG<1HHHEIIHHIHHIHHIIIIH@IHGHHGIHHHHHIIIIIHHHHFGFGIIIIHIIIHIHGHHH?DDDD MD:Z:94 NH:i:2 HI:i:2 NM:i:0 SM:i:3 XQ:i:40 X2:i:40 XO:Z:UM XG:Z:ext

My main worries are:

1) What program/procedure would be most efficient for running step 3?
2) Does this pipeline somewhat make sense?

[GenoMax]

You could use bbsplit.sh from BBMap to figure this out in one step. Take a look at this thread about how to do this.

If you already have the /nomapping file you should be able to convert back to fastq reads using "reformat.sh" from BBMap suite.

reformat.sh in=file.nomapping out=reads.fq

Then use the reads file to map to viral genome using any aligner you like (including bbmap.sh).