User: irfanwustl
irfanwustl • 20
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Posts by irfanwustl
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... Is there a list of all promoters' genomic positions with gene names? From the UCSC table browser, I can get the annotation. But instead of gene id, this gives transcript_id. Any suggestion, please? ...
written 23 days ago by
irfanwustl • 20
• updated
23 days ago by
rpolicastro ♦ 3.9k
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... Hi,
Given two bed files, I want to get the overlapping feature which has at **most** x bp overlap. Probably I should use closest bed but how to restrict the overlap to some x bp at most? ...
written 23 days ago by
irfanwustl • 20
• updated
23 days ago by
Pierre Lindenbaum ♦ 134k
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... Hi,
We have some Methylation samples and obtained some differentially methylated regions (DMR) from those samples. Now we are asking are those DMR makes biological sense. So we want to know if a DMR is in promoter, gene body, intron, exon, repeat regions, or low complexity regions. To test the promo ...
written 7 weeks ago by
irfanwustl • 20
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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 5 months ago by
irfanwustl • 20
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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 5 months ago by
irfanwustl • 20
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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 5 months ago by
irfanwustl • 20
• updated
5 months ago by
MatthewP • 880
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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 months ago by
irfanwustl • 20
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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 months ago by
irfanwustl • 20
• updated
5 months 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 5 months ago by
irfanwustl • 20
• updated
5 months ago by
ATpoint ♦ 45k
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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 6 months ago by
irfanwustl • 20
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