User: ARich

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ARich60
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United States
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4 months, 3 weeks ago
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4 years, 3 months ago
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Posts by ARich

<prev • 20 results • page 1 of 2 • next >
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enrichment term from clusterprofiler
... Dear Biostar users, I am using clusterprofiler tool for enrichment analysis but its not working with Staphylococcus_aureus (Newman strain) kegg and GO annotation is available on uniprot for locus tags I am using. However when i am using it for clusterprofiler it is not retrieving the function annot ...
rna-seq written 4 months ago by ARich60
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Pathway analysis from MGRAST output
... Hi Biostar community, I am interested to know if there is a tool or software which can take mgrast pathway output and provide list of altered pathways between the groups. and provide nice visualization with good resolution. Thanks! ...
mgrast pathways next-gen written 16 months ago by ARich60
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Comment: A: Software For Determining Pathway Differential Expression For Annotated Ngs Data
... Hi JacobS, I am also interested doing things in same line. Have you got any reply or have found out the solution? ...
written 16 months ago by ARich60
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Answer: A: Viral Data classification
... Thanks for your quick reply. these are illumina reads 2X150. It has bacterial sequences as well. I generated contigs using spades and now would like to see the taxonomic classification only for viruses. I tried downloading all gbvrl files but i dont know how can i created single fasta file out of it ...
written 19 months ago by ARich60
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Viral Data classification
... Hi, I would like to classify my viral contigs could anyone recommend me the best way to that. Also if someone has created viral database for blast? Thanks ...
blast written 19 months ago by ARich60
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Answer: A: kmer for sample list
... Dear Rayan, Thanks Yes i tested it with Spaded it does have metagenomic option optimizing to the best kmer. ...
written 19 months ago by ARich60
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kmer for sample list
... Dear All, I am working with paired end metagenomic illumina data.  I need to know that on providing list file with multiple sample entries does kmergenie decide kmer for all the samples provide in the list or how it treats the sample list? I means for metagenomic assembly is feasible to have one ...
kmergenie written 22 months ago by ARich60
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Metagenome raw data download
... Dear All, I wanted to do test run for metagenomic assembly for this purpose I would like to use some raw data from http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html. I have a very basic question generally all papers provides SRA data and i don't really know what is it means doe ...
genome written 2.6 years ago by ARich60 • updated 2.3 years ago by Biostar ♦♦ 20
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Removing Cage effect
... Hello Biostar, I am doing metagenome analysis on 16srRNA data. During my analysis i am seeing huge cage effect. Can anyone suggest how to overcome this effect. Best, ARich ...
genome forum written 3.1 years ago by ARich60 • updated 3.1 years ago by Sean Davis23k
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Comment: C: How to estimate the metagenome size
... Your information is really helpful because I was focussing more on Metavelvet and Meta-IDBA. Thanks alot   ...
written 3.2 years ago by ARich60

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