User: YanO

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YanO130
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130
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United Kingdom
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1 year, 11 months ago
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5 years, 4 months ago
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Posts by YanO

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Filtering variants in case-control DNA-seq study
... Thanks so much for your thoughts. Is filtering out common germline variants a defnite rule for this type of analysis? What about variants common within my own cohort? I've such a small sample size that rare variants will be hard to verify. Also, I should have been more clear sorry, my controls are h ...
written 23 months ago by YanO130
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Comment: C: Filtering variants in case-control DNA-seq study
... Thanks so much for your reply. Why would I remove common variants from 1000 genomes but not common variants from dbSNP? Should I also remove variants that are common within my own sequencing data? Also, I should have been more clear sorry, my controls are healthy people, not matched normal tissue. E ...
written 23 months ago by YanO130
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Filtering variants in case-control DNA-seq study
... I have a cancer case-control germline DNA sequencing study, 100 cases and 100 healthy controls. I've called my variants, and now I'm looking to filter them. What are the "rules" for filtering out variants present in controls? Is it a strict dumping of all variants present even once in the controls ...
genome dna-seq filtering written 23 months ago by YanO130
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Cancer database with both germline and genome-wide sequencing data
... I am looking for a database where I can find germline, genome-wide/noncoding sequencing data in cancer patients. There are plenty of exome-sequencing studies and somatic variant calls available but I'm having real trouble finding something with my exact specifictions of germline & genome-wide/n ...
genome database cancer sequencing written 2.4 years ago by YanO130 • updated 2.4 years ago by Samuel Brady300
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Comment: C: Working with bowtie legacy output
... Just managed to get access to seqanswers now - thanks so much! ...
written 3.2 years ago by YanO130
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Working with bowtie legacy output
... Hi all, I currently am working with some old data, from 2010. It is in what I think is the old legacy bow tie output. The file extension is sample1.bowtie.align.txt.gz. Does anyone know how to convert this format into a different format? I'll take literally any other format: sam/bam/fastq/bigwig.. ...
alignment bowtie written 3.3 years ago by YanO130 • updated 3.3 years ago by Devon Ryan92k
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Comment: C: ngs.plot.r heatmap for single-ntd bed entries
... I suspect the issue here is caused by the fact that your bed file coordinates are only 1bp long. Looks like its stretching this 1bp region to take up most of the plot. I'm not sure how to fix it but try this: if you want to look at this region +- 1000bp, then edit the bed file to be the coordinates ...
written 3.5 years ago by YanO130
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How quantitative is Chip-seq?
... How quantitative is Chip-seq? If it isn't then why do we need normalisation to per million mapped reads? Can we compare the signal across samples if normalised to million mapped reads? I am currently analysing ChIP-seq datasets, and I've been confused by the different attitudes I have come across t ...
normalization chip-seq written 3.5 years ago by YanO130 • updated 3.4 years ago by Fidel1.9k
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Defining ChIP-seq target genes: is there a robust cut-off?
... I am trying to identify the target genes of my transcription factor after ChIP-seq. I have called the peaks and I have also looked at the number of reads falling around the Transcription Start Site of each gene. I am wondering how to define if a gene is bound by my TF. Does it make sense to do th ...
chip-seq written 3.6 years ago by YanO130 • updated 3.6 years ago by Ido Tamir5.0k
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Comment: C: Top MACS peaks from ChIP-seq look identical to input
... Gary thank you so much for such a detailed answer! Much appreciated. I'll have to put a bit more work in to dig out something biologically meaningful from my data so. ...
written 4.5 years ago by YanO130

Latest awards to YanO

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Multiple testing correction with GOstats in R
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to merge replicates in bed file, but keep counts of additional columns?
Appreciated 3.4 years ago, created a post with more than 5 votes. For How quantitative is Chip-seq?
Student 3.5 years ago, asked a question with at least 3 up-votes. For How quantitative is Chip-seq?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Top MACS peaks from ChIP-seq look identical to input
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Top MACS peaks from ChIP-seq look identical to input
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Multiple testing correction with GOstats in R

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