User: Yuyayuya

gravatar for Yuyayuya
Yuyayuya40
Reputation:
40
Status:
New User
Location:
USA
Last seen:
11 hours ago
Joined:
1 year, 2 months ago
Email:
r********@tamu.edu

I'm currently a Ph.D. student and a beginner in bioinformatics. My research focuses on plant breeding and genetics. 

Posts by Yuyayuya

<prev • 14 results • page 1 of 2 • next >
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Orienting contigs/ scaffolds in de novo assembly
... Hello everyone, I'm doing de novo assembly from 150 bp whole genome shotgun reads. My pipeline is: 1. Trimmomatic (trimming and quality filtering) 2. SOAPdenovo2 (de novo assembly) 3. mumMER3 (align to reference sequence). After aligning contigs to reference sequence, I connect the contigs accor ...
assembly written 6 days ago by Yuyayuya40
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HISAT2 alignment for single end read
... I have one set of RNA-seq samples which are single-end read. Can I use `-U` to import my sample to do the alignment in HISAT2? `hisat2 [options]* -x {-1 -2 | -U | --sra-acc } [-S ]` ...
rna-seq written 5 weeks ago by Yuyayuya40 • updated 5 weeks ago by Devon Ryan81k
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Answer: A: Extraction sequence from other sequence
... If the sequence is not too long, you might use `grep` to find the sequence and save to new file by using `>`. I'm not quite sure what's your question. Just guessing... ...
written 5 months ago by Yuyayuya40
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Why alignment in "blat" and "nucmer" are different?
... Hello everyone, I'm doing genome assembly using SOAPdenovo2-MUMmer3 pipeline. After scaffolds were built, I used `nucmer` to align each scaffold to chromosome based on the reference genome. After `nucmer` alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest ...
assembly alignment written 5 months ago by Yuyayuya40
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Answer: A: Strange MA plot from DESeq2
... For those people encounter the same problem like me. Type `plotMA` in R and check the working environment. For example, I got > plotMA function (object, ...) UseMethod("plotMA") It means the `plotMA()` I used isn’t DESeq2’s plotMA function. In this situation, use ` DESeq ...
written 9 months ago by Yuyayuya40
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Comment: C: Strange MA plot from DESeq2
... Thank you, Sir! I'll do that. It may be true since I did have some error when I installed DESeq2. ...
written 9 months ago by Yuyayuya40
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Comment: C: Strange MA plot from DESeq2
... Thanks for replying! I generated the DESeqDataset by combining countData and colData by `DESeqDataSetFromMatrix( )` Here's the entire code I used: > dat = read.csv(file = "/User/Desktop/gene_count_matrix.csv", header = T, row.names=1) > colData = read.table(file = "/User/Deskt ...
written 9 months ago by Yuyayuya40
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Comment: C: Strange MA plot from DESeq2
... Thanks for replying! Here's the session's info: **R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6,** with **DESeq2_1.16.1** ...
written 9 months ago by Yuyayuya40
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Answer: A: How to give directory path in DESeq2
... I always set the directory while reading the data file. For example: dat = read.csv( file = "/Users/zzzz/Desktop/matrix.csv", header = T, row.names=1) ...
written 9 months ago by Yuyayuya40
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Comment: C: Strange MA plot from DESeq2
... Here's the code I used: lncap_de <- DESeq(data_deseq_1) lncap_de_out <- results(lncap_de) res <- results(lncap_de, alpha = 0.05) And, I checked the result by: head(res[ order(resSig$log2FoldChange), ]) It looks like (log2FoldChange seems normal): I tried demo data fro ...
written 9 months ago by Yuyayuya40

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