Mapping metatranscriptomes to MAGs

Question

[pfchuckran]

I am looking to map soil metatranscriptomes against a set of MAGs I have assembled and I was wondering if it would be best practice to either: 1) map reads from my metatranscriptomes against gene calls from MAGs; 2) map against the contigs used to assemble the mags (prior to binning); 3) de novo assemble metatranscriptomes and then align to the metagenomic bins; 4) something else entirely. Any insights would be much appreciated - still very new to this.

Thanks

[361158385]

Hi,

Do you know now how to map the transcriptomes reads to the MAGs? and then calculate the transcript counts or even the specific genes?

Thanks!