User: bsp017

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bsp01720
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Location:
Wales, Bangor, Bangor Uni
Last seen:
2 weeks ago
Joined:
2 years, 10 months ago
Email:
j*******@bangor.ac.uk

Posts by bsp017

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Gage GO annotations vs Entrez
... Thanks for the reply. Same result with NA row names removed: lapply(keggres, head) $greater p.geomean GO:0000009 alpha-1,6-mannosyltransferase activity NA GO:0000010 trans-hexapren ...
written 10 weeks ago by bsp01720
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Gage GO annotations vs Entrez
... Hi all, I'm using Gage v2.28.2 to analyse gene enrichment pathways in RNA-seq data. Genes were initially annotated with entrez ID, which worked fine: kg.eco=kegg.gsets("eco") kg.eco.eg=kegg.gsets("eco", id.type = "entrez") head(kg.eco.eg$kg.sets, 2) keggres = gage(p3, gsets=kg ...
gage gene ontology entrez rna-seq gene enrichment written 10 weeks ago by bsp01720
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Gage duplicate identifiers as row names
... I have a dataset with Enterez gene annotations and log fold change values under different conditions. I would like to do a geneset enrichment analysis with Gage v2.28.0. I am using RStudio. However I'm not sure how to handle duplicate row.names in column 1 I followed the 'Gene set and data preparat ...
gage bacteria kegg rna-seq entrezid written 3 months ago by bsp01720 • updated 3 months ago by h.mon15k
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how to calculate genome coding density
... Hi all, I have just calculated gene coding desnsity across some bacterial genomes. It is coming out quite high at ~87%, I think it is usually around 80%. I simply counted the ATGC's in my .ffn file and subtracted that from the total nucleotide count. When calculating coding density should I includ ...
genome assembly rrna written 9 months ago by bsp01720
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length of combined transcripts
... Hi all, Is there a tool to calculate the combined length of transcripts which map to a given interval. For example as a function of bedtools or htseq? I can calculate the number of reads mapping to a particular gene using these tools but not the length of the gene segment which has been covered. Wh ...
rna-seq written 2.5 years ago by bsp01720 • updated 2.5 years ago by Alex Reynolds23k
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Answer: A: metatranscriptomic read mapping
... In response to my question, I found this paper; http://t.co/snb0U82HVZ which maps metatranscriptome files against an antibiotic resistance gene database. If reads map more than 3 times to a gene and span > 200 bp of that gene then it's considered significant.   ...
written 2.8 years ago by bsp01720
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metatranscriptomic read mapping
... I mapped a depleted metatranscriptome bam file against a reference bacterial genome. Some genes have a 'substantial' number of reads mapping. I have previously isolated this bacteria from the sequencing site. Is there a method where I could say that x number of genes from this bacteria are expressed ...
alignment rna-seq written 2.9 years ago by bsp01720 • updated 2.8 years ago by Brian Bushnell15k

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Popular Question 8 months ago, created a question with more than 1,000 views. For metatranscriptomic read mapping

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