User: irfanwustl

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irfanwustl10
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Posts by irfanwustl

<prev • 19 results • page 1 of 2 • next >
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Comment: C: paired reads aligned at the same genomic position
... Actually, I want to count how many reads aligned to a specific position (like depth) from a python code. That's why I was trying to remove one read. ...
written 28 days ago by irfanwustl10
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How to know the aligned base of a specific position from a read
... What can be an easy way to get the aligned base of a specific position from a read in bam file? If the CIGAR string has only "M", probably we can do it easily. But if the CIGAR string has clipping, deletions, etc. probably this is complicated. Is there a tool to accomplish this? ...
alignment bam written 29 days ago by irfanwustl10
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paired reads aligned at the same genomic position
... We know sometimes paired reads can align at the same position. In such a case, is there any simple command to remove one of the paired reads from the bam file? ...
alignment bam written 29 days ago by irfanwustl10 • updated 29 days ago by MatthewP780
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"C strand" and "G strand" from bisulfite converted bam files
... We know to calculate methylation value for a CpG position from the bam file we have to consider "C strand" and "G strand". I am a little confused about how to determine which read is "C strand" and which is "G strand" from the bam file? It seems a typical bisulfite aligner adds a tag to the bam fil ...
bam methylation bisulfite written 5 weeks ago by irfanwustl10
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Which read should be considered to calculate methylation value?
... I am using [BISCUIT][1] for WGBS data. After the full process BISCUIT provides bedgraph file with CpG and corresponding methylation value. However, I am wondering how BISCUIT figure out which read should be considered in a bam file for methylation value calculation? For example, in the biscuit tview ...
biscuit bam methylation written 5 weeks ago by irfanwustl10 • updated 4 weeks ago by Biostar ♦♦ 20
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Resource for hands on experience
... Hi, I am from computer science background. As I am new to bioinformatics I am wondering is there any resource (book, workshop, blog, online course, etc) focusing on practical aspects of the different biological data? Particularly is there any resource on how to process expression data (both array ba ...
methylation rna-seq written 7 weeks ago by irfanwustl10 • updated 6 weeks ago by ATpoint40k
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Blueprint WGBS pipeline
... I am trying to set up the Blueprint WGBS pipeline. However, I cannot a Github page for the pipeline. All I have found [this][1] which verbally explains the pipeline. Wondering is there any Github page where I can find the pipeline? [1]: http://dcc.blueprint-epigenome.eu/#/md/bs_seq_grch38 ...
sequencing wgbs blueprint written 11 weeks ago by irfanwustl10
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Comment: C: Bedtools intersect with header file
... Got it. Yes, the header was not indicated by '#' ...
written 4 months ago by irfanwustl10
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Comment: C: All CpG position of hg38
... Thanks. I have responded there. However, I was looking for all CpG sites. Not only the island. Is there any annotation for all CpG? ...
written 4 months ago by irfanwustl10
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Comment: A: Bedtools intersect with header file
... Sorry for my late response. Actually, I could not resolve it. Is it a bug? ...
written 4 months ago by irfanwustl10

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