User: ARich

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ARich60
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Posts by ARich

<prev • 26 results • page 1 of 3 • next >
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Comment: 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 12 weeks 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$symbol = mapIds(org.Hs.eg.db, ...
written 12 weeks ago by ARich60
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CluserProfiler message "No gene can be mapped"
... Hi Biostar users, I am working with clusterprofiler enrichKegg function KEGG_all = enrichKEGG(regulated.gene$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 strange messa ...
R written 3 months ago by ARich60
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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 3 months ago by ARich60 • updated 3 months ago by WouterDeCoster29k
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Comment: C: Genome Snp Annotation for non human
... Thank you for the reply I will try this ...
written 7 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 7 months ago by ARich60
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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 13 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 2.1 years 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 2.1 years 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 2.3 years ago by ARich60

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