User: Agaz Hussain Wani

Reputation:
40
Status:
New User
Location:
India
Last seen:
4 months, 1 week ago
Joined:
4 years, 7 months ago
Email:
h************@gmail.com

Posts by Agaz Hussain Wani

<prev • 51 results • page 1 of 6 • next >
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Can I use UCSC genome browser to annotate Epic data
... I have Epic methylation data and was just trying to find annotations for CpGs, however, I don't find some CpGs in the genome browser. I can find some CpGs which I believe may be from 450K data. I would like to know if UCSC browser has Epic CpG annotations. I already have Illumina annotation file f ...
annotation written 4 months ago by Agaz Hussain Wani40
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Comment: C: I want to know if there is reference for brain cell types
... Actually, I want to calculate the cell proportions of the brain-based methylation samples on Epic chip. So I need to have a reference brain cells proportion like the link above for an R package. Is it like that? ...
written 4 months ago by Agaz Hussain Wani40
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Comment: C: I want to know if there is reference for brain cell types
... I am looking for methylation data, can you point me to that. ...
written 4 months ago by Agaz Hussain Wani40
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I want to know if there is reference for brain cell types
... I am curious to know if there exists any database or package that gets us to reference brain cells. Like there are many R packages for blood cell types such as for Epic chips. https://bioconductor.org/packages/release/data/experiment/vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.htm ...
R methylation written 4 months ago by Agaz Hussain Wani40
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Comment: C: Infinium MethylationEPIC BeadChip probes with cross-hybridisation potential
... Thank you for your comment. I already go the data from that paper and was wondering if it is up to date. ...
written 7 months ago by Agaz Hussain Wani40
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Infinium MethylationEPIC BeadChip probes with cross-hybridisation potential
... I would like to get the latest list of probes with cross-hybridization potential Infinium MethylationEPIC BeadChip. I want to download the file and use it to remove the probes before performing any analysis. Can anybody help? ...
epic array written 7 months ago by Agaz Hussain Wani40 • updated 7 months ago by Charles Warden7.5k
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Comment: C: bowtie options for exact match with reference short sequence
... How to tell your tool to extract only the exact matching reads. I have asked the question https://www.biostars.org/p/334795/#335724 ...
written 15 months ago by Agaz Hussain Wani40
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Comment: C: Count exact match reads in SAM file
... Thank you for your comment. I tried using `BBMap` and I used the command `reformat.sh in=output.sam out=exact.fastq`, however, I am not able to find how to extract exact matching reads. The given command extracts all the reads to the new file. ...
written 15 months ago by Agaz Hussain Wani40
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Count exact match reads in SAM file
... I got the alignment result in SAM format using bowtie2. As bowtie2 does not have the setting for exact match, so I want to count the number of exact match. I tried to use `grep` to extract the exact reads using `grep AS:i:0 old.sam >> newfiltered.sam` and when I try to count by `samtools` u ...
exactmatch alignment sam written 15 months ago by Agaz Hussain Wani40
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Comment: C: How to interepet wgsim roc results
... I found a very informative post here http://research.cs.wisc.edu/wham/comparison-using-wgsim/, still comments are welcome. ...
written 21 months ago by Agaz Hussain Wani40

Latest awards to Agaz Hussain Wani

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