User: dnzkursun

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dnzkursun0
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Posts by dnzkursun

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Comment: C: Infer Experiment strand information interpretation
... Then, it is fr-firststrand. Thank you for the link. ...
written 2 hours ago by dnzkursun0
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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 4 hours ago by dnzkursun0 • updated 3 hours ago by genomax73k
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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 11 days ago by dnzkursun0
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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 11 days ago by dnzkursun0
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Comment: C: Truseq Stranded Total RNA and NEBNext Ultra II Directional RNA library prep kit
... Thank you for the comment. I have only tumor samples for Truseq Stranded Total RNA kit. And for NEBNext Ultra II Directional RNA library prep kit I have the same type of tumor samples and also control samples. ...
written 6 weeks ago by dnzkursun0
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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 6 weeks ago by dnzkursun0
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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 5 months ago by dnzkursun0
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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 5 months ago by dnzkursun0
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FFPE-Fresh RNA-seq HG Normalization
... Hello, I am trying to normalize housekeeping genes for FFPE tumor samples and fresh frozen control samples. I am both using the Galaxy platform and Linux command line. Any related comments will be much appreciated Bests, Deniz ...
ffpe housekeepinggene rna-seq normalization written 5 months ago by dnzkursun0
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How to add gene id's to the Cuffnorm output at Galaxy?
... Hello, I am running an RNA-seq pipeline involving Cuffmerge, Cuffcompare, and Cuffnorm tools, at Galaxy main instance, respectively. Even though I add the Gencode annotation files in the Cuffmerge and Cuffcompare steps, I ended up having the tracking id's but not the gene ids of Cuffnorm output f ...
rna-seq written 9 months ago by dnzkursun0

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