User: irfanwustl
irfanwustl • 10
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Posts by irfanwustl
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... 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
irfanwustl • 10
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... 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? ...
written 29 days ago by
irfanwustl • 10
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... 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? ...
written 29 days ago by
irfanwustl • 10
• updated
29 days ago by
MatthewP • 780
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... 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 ...
written 5 weeks ago by
irfanwustl • 10
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... 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 ...
written 5 weeks ago by
irfanwustl • 10
• updated
4 weeks ago by
Biostar ♦♦ 20
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... 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 ...
written 7 weeks ago by
irfanwustl • 10
• updated
6 weeks ago by
ATpoint ♦ 40k
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... 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 ...
written 11 weeks ago by
irfanwustl • 10
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... Got it. Yes, the header was not indicated by '#' ...
written 4 months ago by
irfanwustl • 10
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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
irfanwustl • 10
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... Sorry for my late response. Actually, I could not resolve it. Is it a bug? ...
written 4 months ago by
irfanwustl • 10
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