User: ARich

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ARich60
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60
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United States
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5 years, 11 months ago
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Posts by ARich

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Binned input for Megan
... Means reads which are assembled with Spades are then binned based on compositional and taxonomic similarity using CONCOCT,Maxbin etc ...
written 6 days ago by ARich60
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Binned input for Megan
... Dear Biostar users, I have very basic question regarding megan input. I would like classify my binned reads using megan. The question is can i use these binned reads for blastx against nt database or blasting contigs against NT database in only appropriate? Thank you in advance! ...
assembly written 7 days ago by ARich60 • updated 1 day ago by colindaven1.2k
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Comment: C: Metagenomics assembly comparison
... Thank you for these paper. They were really helpful. I have another question regarding workflows. I am always confused with the workflow because each one has its own. Can you suggest me something more standard in term of taxonomic and functional classification. I have understood two workflows by go ...
written 7 days ago by ARich60
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Metagenomics assembly comparison
... Dear Biostar user, I have a question regarding metagenomics assemby stats. I ran megahit and metaSpades on one sample (paired end) Then I ran metaquast to test out of these two assemblers which one is providing better statistics. Currently the output is bit confusing to know which one i should cho ...
assembly written 5 weeks ago by ARich60 • updated 5 weeks ago by h.mon25k
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Answer: C: CluserProfiler message "No gene can be mapped"
... I got the answer to my problem. I was using some cutoff. After the cutoff few comparison had no genes left for down-regulated list This was kind of warning message more that a error. ...
written 14 months ago by ARich60
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Comment: C: CluserProfiler message "No gene can be mapped"
... I am quite sure. The reason is because I cant ever find these IDs in my file. `--> No gene can be mapped.... --> Expected input gene ID: 7364,127,574537,5538,4351,221 --> return NULL... ` I used standard conversion from of Symbols to Entrez ids. `res$symbol = mapIds(org.Hs.eg.db, ...
written 14 months ago by ARich60
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CluserProfiler message "No gene can be mapped"
... Hi Biostar users, I am working with clusterprofiler enrichKegg function KEGG_all = enrichKEGG(regulated.gene$entrez, organism="human") I have used `library(org.Hs.eg.db)` to convert gene `names(Symbols)` to Entrez ID which is the possible input to use this function. However I am seeing stran ...
R written 14 months ago by ARich60 • updated 5 months ago by zx87547.3k
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Bundle file for mouse
... Hi All, I am currently struggling with Bundle file for mouse genome (mm10) I searched and found this: http://hgdownload.soe.ucsc.edu/downloads.html#mouse However i am not sure how to use this information and translate it into VCF for GATK? Any kind of suggestion would be of great help! Thanks! ...
next-gen snp written 15 months ago by ARich60 • updated 15 months ago by WouterDeCoster39k
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Comment: C: Genome Snp Annotation for non human
... Thank you for the reply I will try this ...
written 18 months ago by ARich60
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Genome Snp Annotation for non human
... Hi, I am using snpeff for annotation of Candida albicans. For RefSeq genome the snpeff annotation worked well. Now I am using different source for genome http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/ and SnpEff is not working. With this genome I am not abl ...
genome snp written 18 months ago by ARich60

Latest awards to ARich

Popular Question 14 months ago, created a question with more than 1,000 views. For kmer for sample list
Popular Question 14 months ago, created a question with more than 1,000 views. For How to estimate the metagenome size
Popular Question 14 months ago, created a question with more than 1,000 views. For Unequal Sample Number
Scholar 14 months ago, created an answer that has been accepted. For C: CluserProfiler message "No gene can be mapped"
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to estimate the metagenome size

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