User: Chris_AI

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Chris_AI30
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Posts by Chris_AI

<prev • 16 results • page 1 of 2 • next >
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Comment: C: CpG Density with respect to TSS
... Thanks for the suggestion! I will give it a try! ...
written 13 days ago by Chris_AI30
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CpG Density with respect to TSS
... Dear all, I would like to replicate an analysis from the paper "[Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing"][1]. In more detail, I try to reproduce the plot 1a. Does anyone of you know, how this plot has been created. I am struggling to calculate the den ...
R ngs density methylation sequencing written 13 days ago by Chris_AI30
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Comment: C: Unsupervised method for detecting differentially methylated regions (DMR)
... As far as I know, BSmooth and Bisulfighter detect DMRs based in predefined subgroups. ...
written 5 months ago by Chris_AI30
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Unsupervised method for detecting differentially methylated regions (DMR)
... Dear all, I am working on whole-genome-bisulfite data and would like to detect differentillay methylated regions. When having predefine conditions for each sample (i.e. clinical infromation), this is not a big deal. Since I am working on a more or less mining-project, I would like to know if there ...
bisulfite sequencing written 5 months ago by Chris_AI30
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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 7 months ago by Chris_AI30
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Comment: C: Coordinates for Transcription Start Site (TSS)
... Let's see if it helps, thanks for the idea! ...
written 7 months ago by Chris_AI30
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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 7 months ago by Chris_AI30
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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 7 months ago by Chris_AI30 • updated 7 months ago by YaGalbi1.3k
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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 9 months ago by Chris_AI30 • updated 9 months ago by Devon Ryan81k
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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 10 months ago by Chris_AI30

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