User: Zhilong Jia

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Zhilong Jia1.6k
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a bioinformatician

Posts by Zhilong Jia

<prev • 247 results • page 1 of 25 • next >
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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 Jia1.6k
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Comment: C: Edit a Multifasta File Through awk
... No, just show the content of the files to clarify `1.txt` and `2.txt` . ...
written 3 months ago by Zhilong Jia1.6k
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Answer: A: Edit a Multifasta File Through awk
... `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 Jia1.6k
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Tools to infer population structure and evolution from structural variation genotype data
... 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 ...
population structure structural variation written 12 months ago by Zhilong Jia1.6k • updated 10 months ago by Biostar ♦♦ 20
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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 Jia1.6k
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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 Jia1.6k
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Comment: C: edger model matrix design of linear model
... 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 Jia1.6k
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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 Jia1.6k
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Answer: A: A good pipeline for GO term analysis on RNA-seq Clusters in R?
... 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 Jia1.6k
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Comment: C: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expressi
... 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 Jia1.6k

Latest awards to Zhilong Jia

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Popular Question 9 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Scholar 9 months ago, created an answer that has been accepted. For A: Batch effect removal before merging microarray data sets
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics

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