Hey there!
I'm new to using MALT and I'm confused about the mapping files. I think I want to use accession to taxonomy (-a2taxonomy) but...
22 results in 0.0031 seconds.
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correlate taxa with the gene function
Hi,
I am doing a project on metatranscriptomics. I followed the Trinity tutorial for doing differential gene expression and annotations.... -
MALT/MEGAN question
Hello all,
I'm trying to use MALT/MEGAN for the first time through ubuntu. I have a FASTA file of some shotgun microbial sequences that I... -
Parsing a MEGAN file by command line
Hi, I have a quite large RMA file (about 40 GBs), and every time I try to open it, my (poor little) PC freezes. I was wondering if there's a way to parse... -
MEGAN - changing query coverage?
Hello,
Does anyone know if it is possible to change the parameters in MEGAN to only consider fragments with 100% query coverage?
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How to assign "Not assigned" BLAST hits by MEGAN
Hello experts,
I want to classify several millions of pathogen DNA/cDNA reads to taxonomical groups (like bacterial, viral, fungal ...).... -
How to combine taxonomy with functions using MEGAN?
Hi SEQanswer community,
I am trying to combine the two different views of Taxonomy and Functional (KEGG and SEED) annotation using MEG... -
sam2rma Tool in MEGAN
Has anyone been able to use the sam2rma standalone tool provided with MEGAN? I can't seem to get it to perform taxonomic classification, although I can... -
megan5:Parse error: java.util.NoSuchElementException
Hi,
I had got error while uploading the blastp in the new Version 5.8.6 build 13 feb 2015. But when the same blastp is uploaded in to the... -
importing sam files from bowtie to megan
hi all,
i used bowtie2 (through Taxoner) to align a bacterial community metatranscriptome (rna-seq sequenced by HISEQ).
now i am trying... -
Questions: Reads scores for RDP Classifier files imported into MEGAN
Hi ALL! I'm new to this forum, and also new to the world of metagenomics data analysing.
I would appreciate if anyone can enlighten me on this question....
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MEGAN - how many BLAST hits to keep for each?
Hi
I'm wondering if I could get some advice for experts on this forum. I am working with the Illumina metagenomic dataset and using MEGAN... -
Megan for contig or gene classification
Hi SEQanswers experts,
I've used megan extensively to taxonomically classify reads from metagenomes which is, according to the initial... -
MEGAN view alignment problems
In the past I've been able to select a node in a MEGAN taxonomy tree, and view alignments of the reads in that node to the better BLAST hits. However,... -
Metagenomics - MG-RAST --> MEGAN
Does anyone if it's possible to grab output from MG-RAST's pipeline and feed it into MEGAN?
The all vs. all BLAST search required for...
