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ablab / metaGT

Pipeline for metagenome and metatranscriptome joint assembly
MIT License
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Inquiry regarding the prepare of raw sequence data in metatranscriptomics #2

Closed Lafmas closed 1 year ago

Lafmas commented 1 year ago

Hello!

Recently, while I was researching metatranscriptomics, I came across the metaGT tool that you developed. I am writing to inquire if there is a specific manual for metaGT available. I have read the paper published in Frontiers, however, I did not comprehend it well as I am a beginner in the NGS field.

My question is, how should I prepare raw sequence files for metatranscriptomics? For metagenomics, our plan is to prepare raw fastq files using shotgun sequencing.

Thank you for your time and I look forward to hearing from you soon.

Best regards, Lafmas

andrewprzh commented 1 year ago

Dear @Lafmas

For metatranscriptomic data MetaGT similarly expects raw FASTQ files from Illumina sequencer. It also expects reads to be adapter-trimmed, but it is usually done automatically by the sequencer.

To get information about the pipeline you can clone GitHub repository and run 

nextflow run metaGT --help

I will add all the information to the README soon. Thank you for pointing that out!

Best Andrey

Lafmas commented 1 year ago

Thank!

Then, could you please recommend whether single-end or paired-end sequencing is better for metatranscriptomic data in metaGT? The read length will be 150 bp.

Best regards, Lafmas

Lafmas commented 1 year ago

I have one more question.

Is it possible to install metaGT using Bioconda rather than cloning the repository from Git?

Best regards, Lafmas

andrewprzh commented 1 year ago

Then, could you please recommend whether single-end or paired-end sequencing is better for metatranscriptomic data in metaGT? The read length will be 150 bp.

MetaGT uses rnaSPAdes inside to perfrom draft transcriptome assembly. Based on my experience paired-end reads typically give noticeably better results (especially for eukaryotic samples). However, if you work with batcterial community the difference may less significant. I'd vote for paired-end reads, but it also depends on the cost etc.

Is it possible to install metaGT using Bioconda rather than cloning the repository from Git?

Not yet, but we'll figure it out at some point.

Best Andrey

Lafmas commented 1 year ago

Thank you for your kind reply!

I`ll prepare pair-end reads and install using git clone.

Best Lafmas