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Hi CAMISIM team,
First, thank you for developing and maintaining such a valuable tool! I am currently working with CAMI 2 challenge data sets and would like to simulate metatranscriptomes to accomp…
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I tried running the DIAMOND_subsystems_analysis_counter.py script with the diamond .m8 output I generated by annotating against the subsystems database but I keep getting this message:
File "/work…
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Hi,
I am using diamond blastx to map metatranscriptomic reads to a single species proteome (Salmonella enterica). Currently, I see many reads that cover only a tiny part of a target protein, because …
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Hi,
I am trying to run mmseq-linux v1.0.9 using a large metatranscriptomics dataset as reference (>4 million ORFs). The run stops after saying “Amalgamating transcripts and calculating summary stat…
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### Description of bug
I am running the following command "spades.py --rna -s mouse1_mRNA.fastq -o mouse1_spades -m 50 --phred-offset 33" getting error like this == Error == system call for: "['/hom…
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I've been developing a metagenomic/metatranscriptomics software suite called VEBA (https://github.com/jolespin/veba) that natively handles eukaryotic binning of metagenome-assembled genomes and exon-a…
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[//]: # (You can add comment regarding your issue hereafter)
### Comments
Transcriptomics is currently a direct child of both Gene expression and Transcriptomics, which is itself a direct child of G…
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Hello, in the literatures I read, Trinity is widely used for the transcriptomics of a single species, especially for the sepcies without reference genome.
So can Trinity be used for the assembly of…
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Hello,
I'm Sebastian, working on my MSc thesis, aiming to create a knowledge graph of the wastewater treatment microbiome. We're using Netcomi for constructing Microbial Association Networks (MANs)…
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+ Quantify against CDS seqeunces
+ reasoning: microbes express polycistronic transcripts, but genomic rearrangements and other biology between strains makes it hard to have good references at the…