User: dnzkursun

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dnzkursun10
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Posts by dnzkursun

<prev • 12 results • page 1 of 2 • next >
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Comment: C: From DESeq2 normalized counts to heatmap in R
... Thank you very much for providing all the necessary information. ...
written 9 months ago by dnzkursun10
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From DESeq2 normalized counts to heatmap in R
... Hi, I have normalized counts data and DESeq2 result file (including log2FC and Padj values) of each sample. And I want to generate a heatmap of significantly differentially expressed genes (FDR<0.05; log2FC>2) in R studio. However, I could not be sure how to filter the significantly expressed ...
deseq2 rna-seq heatmap written 9 months ago by dnzkursun10 • updated 9 months ago by i.sudbery8.3k
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Comment: C: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da
... Hi, the post is more than 3 years ago but I have a question regarding this pipeline. I want to identify differentially expresses lncRNAs and also protein-coding genes. Therefore, is it doable to use a comprehensive gene annotation file eg hg38 or gencode.v29 at step 3 (alignment/assembly) and then ...
written 9 months ago by dnzkursun10
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Comment: C: Infer Experiment strand information interpretation
... Then, it is fr-firststrand. Thank you for the link. ...
written 9 months ago by dnzkursun10
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Infer Experiment strand information interpretation
... Hi, Below is the result of RSeQC Infer Experiment. Sorry for the such a naive question but I want to make sure if the library type is reverse stranded (aka fr-firststrand, RF) before moving on the analysis. This is PairEnd Data Fraction of reads failed to determine: 0.0087 Fraction of read ...
stranded rna-seq rseqc written 9 months ago by dnzkursun10 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Galaxy DE lncRNA analysis pipeline
... Thank you for the suggestions. Unfortunately, Ballgown is not implemented yet in the usegalaxy.org, and I am not experienced enough to the Ballgown analysis in R. The alternative analysis pipeline which also available in galaxy I am considering, is the "Hisat2-feature counts-DESeq2" pipeline. The tu ...
written 9 months ago by dnzkursun10
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Galaxy DE lncRNA analysis pipeline
... Hi, I am trying to identify differentially expressed lncRNAs in tumor samples (18 replicates) compared to control samples (3 replicates). The same library prep kit is used for all samples; however, 10 samples have 100 bp paired-end reads and others 150 bp pe reads. I am planning to use Cutadapt too ...
galaxy rna-seq lncrna written 9 months ago by dnzkursun10 • updated 9 months ago by Biostar ♦♦ 20
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Truseq Stranded Total RNA and NEBNext Ultra II Directional RNA library prep kit
... Hi, Has anyone try to analyze the RNA-seq data from Illumina **Truseq Stranded Total RNA** kit and **NEBNext Ultra II Directional RNA library prep** kit together? If so, can you please give some suggestion about the normalization of the data which acquired from these two different library prep kits ...
nebnext ultra ii truseq stranded rna-seq written 11 months ago by dnzkursun10 • updated 8 months ago by ATpoint36k
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Comment: A: FFPE-Fresh RNA-seq HG Normalization
... I started the analysis at the Galaxy platform. Since I had limited storage I used 3 FFPE tumors and 3 Fresh Frozen control paired-end samples first and then performed Below table demonstrates the DESeq2 results of FFPE samples as first-factor level and fresh samples as second factor level. &g ...
written 15 months ago by dnzkursun10
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Comment: C: FFPE-Fresh RNA-seq HG Normalization
... Thank you for your reply. I have actually tried both DESeq2 and edgeR tools and used HISAT2 for alignment. However, the housekeeping gene fold change difference did not correlate good enough between FFPE and fresh frozen samples. As far as I know, people are using geNorm and NormFinder algorithm ...
written 15 months ago by dnzkursun10

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