User: Chris_AI

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Chris_AI20
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Posts by Chris_AI

<prev • 12 results • page 1 of 2 • next >
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Differentially methylated regions (DMRs) for a multi group comparison
... Dear all, I am dealing with Whole-Genome-Bisulfite data and currently I am interested in DMRs. I have six tumor types and each tumor type has more than two subgroups. Since I would like to perform a intra- and inter-tumor analysis, a pairwise comparison for diff. methylated regions between tumors a ...
bisulfite seq methylation sequencing written 2 days ago by Chris_AI20
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Comment: C: Coordinates for Transcription Start Site (TSS)
... Let's see if it helps, thanks for the idea! ...
written 11 days ago by Chris_AI20
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Comment: C: Coordinates for Transcription Start Site (TSS)
... Do you assume that the transcription start site is the same as the transcript start (= first nucleotide of the transcript)? ...
written 11 days ago by Chris_AI20
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Coordinates for Transcription Start Site (TSS)
... Dear all, I am working with the gene annotation hg19 (ensembl release 74). I would like to get the TSS for each gene. For the most recent release of hg19, Ensembl provides the transcription start site, but not for release 74. Do you know, where I can get this information from? Using the first base ...
rna-seq written 14 days ago by Chris_AI20 • updated 14 days ago by kennethcondon2007970
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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 8 weeks ago by Chris_AI20 • updated 8 weeks ago by Devon Ryan74k
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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 3 months 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 3 months 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 3 months ago by Chris_AI20 • updated 3 months ago by igor4.9k
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Answer: A: Any tools to quantify intron retention in RNAseq data?
... Try this: https://github.com/williamritchie/IRFinder ...
written 3 months 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 3 months ago by Chris_AI20

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