Can mTAGs be used with transcriptomic data?

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Can mTAGs be used with transcriptomic data? #2

Closed lavi3948 closed 5 days ago

lavi3948 commented 1 year ago

Hello, can MTAGs be used with metatranscriptomic data? When I tried, I got the following message: 2023-03-10 17:29:08,695 ERROR: Command hmmsearch --cpu 4 -o mtags/clean_21_1_R1_qual.fastq_fw.fasta_ssu.hmmer --domtblout mtags/clean_21_1_R1_qual.fastq_fw.fasta_ssu.dom -E 0.01 /projects/lavi3948/software/anaconda/envs/mtags/lib/python3.7/site-packages/mTAGs/data/ssu.hmm mtags/clean_21_1_R1_qual.fastq_fw.fasta failed with message: None 2023-03-10 17:29:08,696 INFO: mTAGs finished with error code 1

hjruscheweyh commented 5 months ago

Dear @lavi3948

mTAGs can work with metatranscriptomic data for detection. Just keep in mind that rRNA is often removed from metatranscriptomic data which means that you will have only very few hits which can will not be representative for the species in your sample.

best, Hans