User: dazhudou1122

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dazhudou112240
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4 days, 18 hours ago
Joined:
2 years, 10 months ago
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Posts by dazhudou1122

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Download all assemblies in a bioproject
... Thank you! That's very helpful! ...
written 4 days ago by dazhudou112240
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Comment: C: Download all assemblies in a bioproject
... Thank you genomax! It is a really nice way to do it! But I will need the translated protein sequences files (faa files) and this method does not seem to be able to do that...am I missing something? ...
written 4 days ago by dazhudou112240
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Comment: C: Download all assemblies in a bioproject
... Thank you so much! I was trying to download every using method (1) but I encountered the following error (up to the "> list_asm.txt" part) : Can't locate JSON/PP.pm in @INC (@INC contains: /home2/s154806/edirect/aux/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor ...
written 4 days ago by dazhudou112240
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Download all assemblies in a bioproject
... Dear Biostars community, I am trying to download all the assembly in a bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=474907 Can anyone tell me how to download them all without manually copying the link and download the assembly like this: wget --recursive -e robots=off --reject "index ...
assembly written 4 days ago by dazhudou112240 • updated 4 days ago by genomax68k
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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 months ago by dazhudou112240 • updated 5 months ago by Kevin Blighe44k
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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 6 months ago by dazhudou112240 • updated 6 months ago by Charles Warden6.9k
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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 10 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 21 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 21 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 21 months ago by dazhudou112240

Latest awards to dazhudou1122

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Most reads counted by HTSeq are "unaligned"
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2 Heatmap issue
Popular Question 3 months ago, created a question with more than 1,000 views. For Most reads counted by HTSeq are "unaligned"
Popular Question 4 months 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 Most reads counted by HTSeq are "unaligned"
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 Heatmap issue
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2 Heatmap issue
Popular Question 21 months ago, created a question with more than 1,000 views. For KEGG pathway maps
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2 paired analysis

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