The setting of the parameter - -in-gn when using the metatranscriptomic reads

[B-1991-ing]

Hi Zhichao,

What should we take as the input for the parameter - -in-gn when we set -rt metaT? Or we don't need to use the parameter - -in-gn when taking the metatranscriptomic reads?

Best,

Bing

[ChaoLab]

The input of "--in-gn" should be the location of FOLDER containing the fasta files of input genomes

[B-1991-ing]

But, the MAG are not assembled from the metatranscriptomic reads, they are relatively independent with the metatranscriptomic data.

[B-1991-ing]

What we want to see is how both gene abundance – and especially gene expression – of the different genes.

[ChaoLab]

Metatranscriptomic reads can be mapped onto MAGs since the genomic DNA will be transcribed into RNA. So biologically, this makes sense

[B-1991-ing]

Thank you for your brief explanation, I will give it a try.

[B-1991-ing]

Hi Zhichao,

What is the difference between taking the assembled MAGs & the corresponding metagenome reads where the MAG were assembled from and taking the assembled MAGs & the metatranscriptome reads as the input of the metabolic software? I did both.

Does the MW-score_result.txt from the assembled MAGs & the corresponding metagenome reads can let us look all genes’ expression in each pathway at the genome level? Does the MW-score_result.txt from the assembled MAGs & the corresponding metatranscriptome reads can let us look all genes’ expression in each pathway at the transcriptome level?

Or we maybe need to do the gene expression by ourself using the All_gene_collections_mapped.depth.txt and All_gene_collections_transcript_coverage.txt, respectively?

Best,

Bing

[ChaoLab]

Hi Zhichao,

What is the difference between taking the assembled MAGs & the corresponding metagenome reads where the MAG were assembled from and taking the assembled MAGs & the metatranscriptome reads as the input of the metabolic software? I did both.

Does the MW-score_result.txt from the assembled MAGs & the corresponding metagenome reads can let us look all genes’ expression in each pathway at the genome level? Does the MW-score_result.txt from the assembled MAGs & the corresponding metatranscriptome reads can let us look all genes’ expression in each pathway at the transcriptome level?

Or we maybe need to do the gene expression by ourself using the All_gene_collections_mapped.depth.txt and All_gene_collections_transcript_coverage.txt, respectively?

Best,

Bing

Yes, you will need to do gene expression by yourself using those two txt files.

MW-score gave you another metric to compare between different samples.

[B-1991-ing]

Yes, you will need to do gene expression by yourself using those two txt files.

What kind of figure is best to display all gene expressions in one pathway at a ‘genome’ and ‘transcriptome’ level? Hetamap or Manhattan?

[ChaoLab]

I have no experience in using Manhattan chart (maybe it is new), I suggest heatmap

[B-1991-ing]

I plotted the gene coverage of each MAG in each 'genome' or 'metagenome' in two heatmaps.

The All_gene_collections_transcript_coverage.txt is the gene coverage of all MAG contigs across all metatranscriptome samples? The we can see the gene coverage of all genes across all metatranscriptome samples also?

[ChaoLab]

It is the gene (transcript for metatranscriptome) coverage of all MAG genes. METABOLIC only does metagenomic/metatranscriptomic mapping based on all genes