User: irfanwustl

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irfanwustl20
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Posts by irfanwustl

<prev • 22 results • page 1 of 3 • next >
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List of all promoter position
... 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? ...
gene written 23 days ago by irfanwustl20 • updated 23 days ago by rpolicastro3.9k
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Get overlapping features with certain fraction max
... 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? ...
genome bedtools written 23 days ago by irfanwustl20 • updated 23 days ago by Pierre Lindenbaum134k
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Genomic position to genomic feature
... 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 ...
genome methylation dmr written 7 weeks ago by irfanwustl20
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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 5 months ago by irfanwustl20
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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 5 months ago by irfanwustl20
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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 5 months ago by irfanwustl20 • updated 5 months ago by MatthewP880
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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 months ago by irfanwustl20
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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 months ago by irfanwustl20 • updated 5 months 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 5 months ago by irfanwustl20 • updated 5 months ago by ATpoint45k
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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 6 months ago by irfanwustl20

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Popular Question 3 months ago, created a question with more than 1,000 views. For cram to bam conversion

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