User: Zhilong Jia
Zhilong Jia • 1.6k
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a bioinformatician
Posts by Zhilong Jia
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2
votes
1
answer
87
views
1
answers
Answer:
A: RNA-seq STAR genome mapping
... it seems you did not install [STAR][1]. what you used probably is [star][2].
[1]: https://github.com/alexdobin/STAR
[2]: https://docs.zmanda.com/Star ...
written 4 days ago by
Zhilong Jia • 1.6k
0
votes
1
answer
180
views
1
answers
... No, just show the content of the files to clarify `1.txt` and `2.txt` . ...
written 3 months ago by
Zhilong Jia • 1.6k
0
votes
1
answer
180
views
1
answers
... `cat 1.txt`
```
TRINITY_DN10231_c0_g1_i1 UBQ5_TOBAC
TRINITY_DN10231_c0_g1_i2 UBQ5_TOBAC
```
`cat 2.txt`
```
>TRINITY_DN10231_c0_g1_i1 len=1399 path=[0:0-908 1:909-912 2:913-1398]
ATATATATATAT
>TRINITY_DN10231_c0_g1_i2 len=1399 path=[0:0-908 1:909-912 2:913-1398]
GGCGCGCGGAGAGA ...
written 3 months ago by
Zhilong Jia • 1.6k
0
votes
0
answers
233
views
0
answers
... Are there tools to infer population structure and evolution from structural variation genotype data?
Generally, [fastStructure][1] or other tools are designed for SNPs. Are inferring population structure and evolution from structural variation genotype data largely different from that from SNP gen ...
written 12 months ago by
Zhilong Jia • 1.6k
• updated
10 months ago by
Biostar ♦♦ 20
0
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2
answers
10k
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2
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Comment:
C: Downloading Data From Mg-Rast
... http://api.metagenomics.anl.gov/metadata/export/mgp128
ref: http://api-ui.mg-rast.org/api.html#sample ...
written 2.1 years ago by
Zhilong Jia • 1.6k
0
votes
2
answers
10k
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2
answers
Comment:
C: Downloading Data From Mg-Rast
... File 050.2 - This is the unfiltered metagenome that was originally uploaded to MG-RAST
File 100.1 - preprocess.passed.fna
File 100.2 - preprocess.removed (low quality)
File 350.2 & 350.3 - These are the protein coding genes (amino acids and nucleotides)
File 440.1 - These are ...
written 2.1 years ago by
Zhilong Jia • 1.6k
0
votes
1
answer
2.5k
views
1
answers
... in line 4, it should be: ` foo <- data.frame(SampleType = paste0(rep(c("A","B"), each = 3)), Reps = rep(1:3, 2),` `Names = paste0(rep(c("A","B"), each=3), rep(1:3, 2) ) )`
`set.seed()` before generating the data will be helpful.
...
written 2.2 years ago by
Zhilong Jia • 1.6k
0
votes
1
answer
2.6k
views
1
answers
Answer:
A: RNA-seq cluster analysis in R
... 0. [clusterProfiler][1]. [Visualization of profile comparison][2] section from Bioconductor package `clusterProfiler`. A quick solution for your question.
see ![figure][3].
1. [co-expressed gene set enrichment analysis, cogena][4]. `cogena` started with gene expression not clustered genes, While i ...
written 2.2 years ago by
Zhilong Jia • 1.6k
1
vote
3
answers
3.2k
views
3
answers
... 0. [the toppcluster webserver][1], but not work recently.
1. [co-expressed gene set enrichment analysis, cogena][2]. But Zebrafish GO gene sets as a gmt file are needed.
2. clusterProfiler. `GO analyses (groupGO(), enrichGO() and gseGO()) support organisms that have an OrgDb object available.` so it ...
written 2.2 years ago by
Zhilong Jia • 1.6k
0
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0
answers
3.0k
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0
answers
... 1. try to download it at the deployed website. you will see the downloaded files as follow.
![enter image description here][1]
2. `The expression profile data should be processed data, in which the fold change of one gene between group A and group B could be calculated with ValueA/ValueB`. Actually ...
written 2.2 years ago by
Zhilong Jia • 1.6k
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