User: Ahmed Alhendi

gravatar for Ahmed Alhendi
Reputation:
40
Status:
New User
Location:
University of Southampton, UK
Website:
https://ahmedalhendi0....
Twitter:
@ahmed_alhendi0
Last seen:
1 day, 6 hours ago
Joined:
1 year, 2 months ago
Email:
m************@gmail.com

Research Fellow in Bioinformatics. A highly motivated research scientist. Interested in cancer research and genome-wide analysis. PhD in Genetics and Genome Biology.

Posts by Ahmed Alhendi

<prev • 10 results • page 1 of 1 • next >
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Answer: A: How To Write Data In A Granges Object To A Bed File.
... Simply, all what you need to do is to use the `as.data.frame()` function to keep all the metadata columns! ```R gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges = IRanges(1:10, end = 7:16), strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2 ...
written 5 weeks ago by Ahmed Alhendi40
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Comment: C: extract and generate a VCF file with only "PASS"
... I like bcftools, it is so fast and can handel larege vcf files from whole genome sequencing (WGS) with high efficiency. However, the bcftools option ```-i 'ID="PASS"'``` will not work for all versions of vcf files, at least it did not work with me with illumenia WGS SNV.vcf files. To make sure it ...
written 3 months ago by Ahmed Alhendi40
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Answer: A: How Can I Plot A Region'S Depth As Follow? While Tools Should I Use?
... You can try Gviz R/bioconductor https://www.bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html It cab be used to to plot Sequencing Depth directly from bam file. ![enter image description here][1] [1]: https://github.com/AAlhendi1707/Images/blob/master/xCapture.PNG?raw=True ...
written 3 months ago by Ahmed Alhendi40
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Answer: A: extract and generate a VCF file with only "PASS"
... If you only want to filter for PASS records then you don't need to use 'AWK '. This simply can be done using bcftools. ``` bcftools view -f PASS input.vcf > output.vcf ``` ...
written 3 months ago by Ahmed Alhendi40
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Comment: C: How to convert featureCounts to FPKM?
... Try [countToFPKM](https://github.com/AAlhendi1707/countToFPKM) package. ...
written 13 months ago by Ahmed Alhendi40
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Answer: A: How to convert featureCounts to FPKM?
... Try [countToFPKM][1] package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. Implements the following equation: ![enter image description here][2]. The `fpkm()` function requires three inpu ...
written 13 months ago by Ahmed Alhendi40
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Answer: A: How to perform FPKM on raw reads in R
... Try [countToFPKM][1] package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. It also provides the user with a reliable function to generate FPKM heatmap plot of the highly variable features in R ...
written 14 months ago by Ahmed Alhendi40
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Answer: A: Calculating FPKM after htseq-count
... Try [countToFPKM][1] package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. Implements the following equation: ![enter image description here][2]. The `fpkm()` function requires three inpu ...
written 14 months ago by Ahmed Alhendi40
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Answer: A: htseq-counts output merge into one matrix ??
... This is easily done using R script! You can use my R script on https://github.com/AAlhendi1707/htseq-merge/blob/master/htseq-merge_all.R For more details about how to generate and combine HTSeq outputs into one read count matrix in R https://ahmedalhendi0.wordpress.com/2019/03/20/combine-htseq-out ...
written 14 months ago by Ahmed Alhendi40
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Comment: C: htseq-counts output merge into one matrix ??
... You can use my R script on https://github.com/AAlhendi1707/htseq-merge/blob/master/htseq-merge_all.R ...
written 14 months ago by Ahmed Alhendi40

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