User: dazhudou1122

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dazhudou112240
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Posts by dazhudou1122

<prev • 35 results • page 1 of 4 • next >
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DESeq2 multiple group comparison
... Dear Biostars community: I ran into a question when I was doing RNA-seq analysis using DeSEQ2. I have 4 groups, 3 samples per group, and set my groups using the following code: (condition <- factor(c(rep("ctl", 3), rep("A", 3), rep("B", 3), rep("C", 3)))) Can anyone tell me how the compar ...
deseq2 rna-seq written 5 weeks ago by dazhudou112240 • updated 5 weeks ago by Kevin Blighe37k
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Profiling taxonomic distribution of genes in human gut microbiome
... Dear Biostars community, I am trying to determine the abundance and taxonomic distribution of a gene cluster in human gut microbiome samples (metagenomic sequencing). I would like to do this using blast (diamond blast). Can you give me suggestions on how to profile the taxonomic distribution of th ...
genome gene next-gen sequencing written 10 weeks ago by dazhudou112240 • updated 10 weeks ago by Charles Warden6.1k
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16S rDNA sequence Silva database
... Dear BioStars Community, I am trying to download the individual 16S rDNA sequence of bacterial strains of interest using the Search function on Silva website as my reference for mapping. When I chose “SSU r132”, “fasta without gaps” and “zip” option, the file I downloaded is the 16 rRNA sequence. ...
sequence written 6 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... It is weird that path.ids, path.ids.l and path.ids2 are all empty. This data set has more than 100 gens that are very significantly differently expressed... ...
written 17 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... Dear cpad0112: Thank you so much for helping! Here are the results: id2eg(ids = toupper(rownames(dds)), category ="SYMBOL", org="mmu") [1] "Note: 8779 of 24062 unique input IDs unmapped." [ reached getOption("max.print") -- omitted 23562 rows ] id.map.refseq <- id2eg(ids = ...
written 17 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... I tried, I used mmu, but no database was downloaded. And if you use mmu as species, then the program does not recognize... ...
written 17 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... Here it is: [1] "Xkr4" "Rp1" "Sox17" "Mrpl15" "Lypla1" "Tcea1" "Rgs20" "Atp6v1h" "Oprk1" "Npbwr1" Thank you:) ...
written 17 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... Thank you! I have modified accordingly:) ...
written 17 months ago by dazhudou112240
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Comment: C: Pathway analysis gene name issue
... I tried but I cant seem to find what mmuNA is.... Here are some examples of the GeneID I have: Geneid Xkr4 Rp1 Sox17 Mrpl15 Lypla1 Tcea1 Rgs20 Atp6v1h Oprk1 Npbwr1 Rb1cc1 Fam150a ...
written 17 months ago by dazhudou112240
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Pathway analysis gene name issue
... Dear BioStars Community, I am a beginner of pathways analysis, and I ran into some issue using gage and pathview. I mapped the RNA-seq (mouse cells) using STAR and counted the feature using featureCounts: featureCounts -T 16 -t exon -g gene_id -a /qbrc/biodata/igenome/Mus_musculus/UCSC/mm1 ...
gene name issue mouse pathway analysis rna-seq written 17 months ago by dazhudou112240

Latest awards to dazhudou1122

Popular Question 16 days ago, created a question with more than 1,000 views. For Most reads counted by HTSeq are "unaligned"
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Most reads counted by HTSeq are "unaligned"
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2 Heatmap issue
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2 Heatmap issue
Popular Question 17 months ago, created a question with more than 1,000 views. For KEGG pathway maps
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2 paired analysis

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