User: Yuyayuya

gravatar for Yuyayuya
Yuyayuya80
Reputation:
80
Status:
New User
Location:
USA
Last seen:
3 weeks, 4 days ago
Joined:
1 year, 6 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 • 15 results • page 1 of 2 • next >
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How to plot SNPs distribution on each chromosome?
... Hello everyone! I want to visualize SNPs results of progeny compared with two parents in the whole genome (to see the introgression regions). For example, plot all the chromosome of progeny and show what regions are from which parent on each chromosome. I guess it should like the figure attached. ...
genome R snp written 6 weeks ago by Yuyayuya80 • updated 6 weeks ago by Alex Reynolds26k
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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 4 months ago by Yuyayuya80
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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 months ago by Yuyayuya80 • updated 5 months ago by Devon Ryan86k
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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 9 months ago by Yuyayuya80
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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 9 months ago by Yuyayuya80
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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 13 months ago by Yuyayuya80
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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 13 months ago by Yuyayuya80
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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 13 months ago by Yuyayuya80
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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 13 months ago by Yuyayuya80
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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 13 months ago by Yuyayuya80

Latest awards to Yuyayuya

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Strange MA plot from DESeq2
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.

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