User: Hoang, Thanh

gravatar for Hoang, Thanh
Hoang, Thanh200
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Last seen:
4 years, 2 months ago
Joined:
4 years, 6 months ago
Email:
h******@miamioh.edu

Posts by Hoang, Thanh

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Mirna-Seq Help
... Hi Calvin, I am analyzing miRNA differential expression from my small RNA sequencing data from mouse tissue using Bowtie > Htseq>Deseq. I tried both whole mouse genome and hairpin miRNA( from miRbase) as reference sequences and annotation of all known miRNA (from miRbase). These worked for me. ...
written 4.2 years ago by Hoang, Thanh200
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Can Tophat Take Snps Into Account?
... Hi, I have been mapping my RNA-seq data to mouse genome from a different mouse strain using TopHat. I am wondering whether TopHat can take SNPs into account during the alignment? ( using SNPs track as an optional input)? Thanks Thanh ...
tophat rna-seq written 4.2 years ago by Hoang, Thanh200 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Non-Coding Rna Annotation
... Hi all, I am analyzing my small RNA sequencing data on mouse tissue. Does anyone know where to download annotation file for non-coding RNA? Thanks Thanh ...
written 4.2 years ago by Hoang, Thanh200 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: Rna-Dna Converter In Fasta Format
... Thank you Bjoern, I figured it out. Just use Fastx nucleotide exchanger.in Fastx-toolkit Thanh On Sun, Sep 22, 2013 at 4:51 AM, Björn Grüning < ...
written 4.2 years ago by Hoang, Thanh200
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Rna-Dna Converter In Fasta Format
... Hi all, I want to to map my sequencing reads to miRNA reference database . Anyone know how to convert RNA to DNA in FASTA format ( U to T) . Thanks Thanh ...
written 4.2 years ago by Hoang, Thanh200 • updated 4.2 years ago by Björn Grüning350
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3' Adapter Trimming Using Fastx-Toolkit Clipper
... Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I want to remove the adapter sequences from the reads before mapping to the genomes/known miRNA database. My 3' adapter sequence is : 5-AGATCGGAAGAGCACACGTCT-3. I found that many reads only contain part of th ...
written 4.2 years ago by Hoang, Thanh200 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: Mirna Analysis
... Thanks Mete and Jenifer for your information. Last time, I did mRNA sequencing analysis and decided to go with TopHat>Htseq>DESeq for DE genes. Just because the results match up quite nicely with my qPCR validation. Although Cuufflink/Cuffdiff produced results with quite similar trend with DE ...
written 4.2 years ago by Hoang, Thanh200
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Mirna Analysis
... Hi all, I would like to analyze my miRNA sequencing analysis from mouse tissue. I have not any idea which tools or pipeline work best. Do you have any suggestion? Regards Thanh ...
written 4.2 years ago by Hoang, Thanh200 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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"Significant" In Cuffdiff'S Ouput
... Hi all, I have some questions about how Cufffdiff does the statistical analysis. I am looking for DE genes in two sample groups ( 3 replicate per group). In the Cuffdiff;s gene_exp.diff, I found many genes that have very large RPKM fold-change between two groups (with p value < or > 0.05) bu ...
cufflinks rna-seq written 4.4 years ago by Hoang, Thanh200 • updated 4.4 years ago by Dave Clements ♦♦ 2.3k
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Comment: C: Exceptionally High Rpkm Values Of Mirna And Other Short Genes In Cuffdiff'S Outp
... Thank you Mohammad and Ross for your valuable information. I am re-running Cuffdiff with No effective length correction and also running EdgeR tool to see how the results go. Thanh ...
written 4.4 years ago by Hoang, Thanh200

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