User: biohack92

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biohack92130
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Posts by biohack92

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Found a raw data file; which -omics technology is this output from?
... My mistake; updated the original post. ...
written 2.3 years ago by biohack92130
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Found a raw data file; which -omics technology is this output from?
... I need to identify where this output file was generated from. I would like to analyze it and I'm 99% sure it's RNA seq data, but I need more information on the generated data before I can identify which bioconductor package would be useful. I appreciate any help. ![enter image description here][1] ...
next-gen rna-seq sequencing written 2.3 years ago by biohack92130
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Is there any reason to analyze plus/minus strands separately in bisulfite seq/methylation data?
... I have bisulfite sequencing data that consists of read count data. The data is split based on strand orientation (plus & minus). What sort of questions can be answered by analyzing the plus/minus strand separately? ...
bisulfite sequencing methylation written 2.8 years ago by biohack92130 • updated 2.8 years ago by Antonio R. Franco4.0k
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Comment: C: ggbio package only works with h19 genome
... I'm getting the same error. Did you find a solution? ...
written 2.8 years ago by biohack92130
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List of exon coordinates from a single Entrez gene ID. Are these exons for alternative splicings of the gene?
... I've done the following: ![enter image description here][1] Basically use the Entrez gene ID to pull the transcripts. Then using the transcript names, extract the exon coordinates. Are each members of this list alternative splicings of the gene? [1]: http://i.imgur.com/QjSaycX.png ...
R bioconductor genomicranges written 2.8 years ago by biohack92130 • updated 2.8 years ago by jotan1.2k
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Comment: C: Is there any way to determine whether my sequenced data uses 0- or 1-based coord
... Thanks for the explanation. ...
written 2.8 years ago by biohack92130
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Is there any way to determine whether my sequenced data uses 0- or 1-based coordinates?
... I have bisulfite sequencing data that was aligned and provided in bigwig format. I've since converted the files to bedgraph format, and based off the naming of the files, the BS-seq data was split by +/- strand (i.e., sample1 has two bedgraph files, one bedgraph for the reads on the plus strand, and ...
genome bed coordinates sequencing bedgraph written 2.9 years ago by biohack92130 • updated 2.9 years ago by Alex Reynolds27k
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Comment: C: How do you remove coverage outliers in sequencing count data?
... Thanks @Devon Ryan. I followed your advice and [this is the plot I created][1]. X-axis shows the # of reads/counts and Y-axis is the frequency of each count. Is there a way to determine which threshold is 'reasonable'? [1]: http://i.imgur.com/Jt3bzJu.png ...
written 2.9 years ago by biohack92130
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How do you remove coverage outliers in sequencing count data?
... I've recently looked at methylation coverage (bisulfite seq data) in IGV, and there are obvious coverage outliers which I'm interpreting as mismappings of repetitive sequences. How do you identify these outliers from methylation calls/count data (I don't have BAM/SAM files) and remove them? ...
R quality control qc bisulfite sequencing written 2.9 years ago by biohack92130 • updated 2.9 years ago by dariober9.9k
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How to calculate correlations across two matrices across samples?
... I have methylation count data in the following two matrices. cov <- matrix(sample(0:7, 100,replace=TRUE), nrow=10, ncol=10) colnames(cov) <- c("group1_1", "group1_2", "group1_3", "group1_4", "group1_5", "group2_1", "group2_2", "group2_3", "group2_4", "group2_5") meth <- matrix( ...
R statistics methylation sequencing written 2.9 years ago by biohack92130 • updated 2.4 years ago by Biostar ♦♦ 20

Latest awards to biohack92

Great Question 2.3 years ago, created a question with more than 5,000 views. For What is a typical workflow to correlate methylation and expression data?
Appreciated 2.8 years ago, created a post with more than 5 votes. For What is a typical workflow to correlate methylation and expression data?
Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For What is a typical workflow to correlate methylation and expression data?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Need Help Interpreting The Percent Identity From Blat M8/9 Output
Student 4.0 years ago, asked a question with at least 3 up-votes. For What is a typical workflow to correlate methylation and expression data?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Need Help Interpreting The Percent Identity From Blat M8/9 Output

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