User: Chris_AI

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Chris_AI20
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Posts by Chris_AI

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STAR/ Bowtie2: number of matched base
... Dear all, I am working on an miRNA pipeline and would like to compare bowtie2 and STAR. STAR has an option, which specifics the minimum number of matches bases to report the aligned read (--outFilterMatchNmin). I try to define the same in bowtie2, but apart from the score functions, I could not fi ...
bowtie2 ngs alignment star written 1 day ago by Chris_AI20 • updated 1 day ago by Devon Ryan71k
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Infer RNA-Seq library preparation from BAM
... Dear all, Do you know a tool, which gives information, if a RNA-Seq library is poly-A or ribosomal depleted? I received a lot of RNA-Data, which has been sequenced in different labs with different libraries. I could check the RNA-SeQC output for the coverage at the 3' and 5' ends, but this will tak ...
ngs rna-seq written 4 weeks ago by Chris_AI20
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Comment: C: Tumor Purity and miRNA / small RNA pipeline
... Yep, it is small rna-seq library. I thought about using RNA-SeQC for the QC step and STAR aligner (with proper parameters). As far as I know, STAR and Bowtie (v1) have quite similar performance, when it comes to short reads, despite the fact that STAR is way faster. ...
written 4 weeks ago by Chris_AI20
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Tumor Purity and miRNA / small RNA pipeline
... Dear all, I would like to ask you for two suggestions: 1. If got an incredible amount of miRNA-Seq data. Can anybody of you recommend a pipline for quality-control and alignment? 2. I would like to compute the tumor purity from whole gnome seq tumor (with matching control) data. I know that it is ...
tumor purity piple rna-seq mirna written 4 weeks ago by Chris_AI20 • updated 4 weeks ago by igor4.6k
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Answer: A: Any tools to quantify intron retention in RNAseq data?
... Try this: https://github.com/williamritchie/IRFinder ...
written 4 weeks ago by Chris_AI20
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Comment: C: Normal pediatric brain samples (RNA-Seq/ Whole-Genome-Bisulfite)
... I know...what is sometimes done is that brain tissue is taken from patients, who died of some condition not related to the nerval system. This is the sad part of the story... ...
written 7 weeks ago by Chris_AI20
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Normal pediatric brain samples (RNA-Seq/ Whole-Genome-Bisulfite)
... Dear fellow researchers, I am struggling with the following problem - I am conducting a study on pediatric brain tumors, but to make my analysis complete, I would need normal/ healthy pediatric brain samples as controls. I searched the internet for public/ non-public data bases, but all I could f ...
next-gen rna-seq sequencing written 7 weeks ago by Chris_AI20 • updated 7 weeks ago by Biostar ♦♦ 20
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Predicting binding probability of circRNA and miRNA
... Dear all, I am working on circular RNA and miRNA. I used the tool DCC to get possible circular RNA candidates from my STAR alignment. Since it is know that circular RNA expression can effect miRNA in various ways (et vice versa), I would like to compute the likelihood that one specific circRNA binds ...
software next-gen rna-seq sequencing written 4 months ago by Chris_AI20 • updated 4 months ago by IP350

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