Align metatranscriptomic RNAseq data to a single reference genome

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3.9 years ago

thorbensieksmeyer • 0

Hi all,

I have metatranscriptomic RNAseq data and I want to align that to a reference genome of a single bacterial species since I know that this particular bacterium is in the mix. I only want to analyse the expression profile of this single species

Can I simply do that with Salmon or STAR aligner or do they also map reads which do not belong to the one species to the reference genome?

Thank you very much for your answers.

RNA-Seq alignment • 701 views

ADD COMMENT • link 3.9 years ago by thorbensieksmeyer • 0

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And how can I do the same but let's say with 2 or 3 different species/strains?

Might this just work?

"You need to make sure that chromosome names are different for the two species in the FASTA files, and the transcript names are different in the GTF files. The chromosome naming should be consistent between FASTA and GTF files for each species. After that, the FASTA files can be concatenated or simply listed one after another (space-separated) in the --genomeFastaFiles The GTF files have to be concatenated into one GTF file."

ADD REPLY • link 3.9 years ago by thorbensieksmeyer • 0

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