User: always_learning
always_learning • 1000
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Posts by always_learning
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... Hi Dear,
Were you able to do that? I wanted to convert my MAF file in Matrix format for Oncoprint as well.
Thanks
Najeeb ...
written 11 days ago by
always_learning • 1000
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Comment:
C: TCGA TMB: What exome size to use?
... Did you get answer to your question? I have been trying to get this answer but so far didn't able to found that. ...
written 5 weeks ago by
always_learning • 1000
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... Hi Florian,
How was your experience with the MACS2 bdgcmp option? I was trying to compare a Tumor and Normal sample ( both having CONTROL Sample) and after running MACS2 bdgcmp option, I am only getting 1-2 DMR peaks ? Is that anything obvious that I am missing?
Thanks ...
written 3 months ago by
always_learning • 1000
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Comment:
C: Best tool for variant calling
... Hi Kevin,
Do you suggest the same pipeline across PANEL and exome data as well?
Thanks
Najeeb ...
written 7 months ago by
always_learning • 1000
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Comment:
C: Best tool for variant calling
... Regarding this point 4:
Produce random BAM subsets per sample (usually 3 subsets at 25%, 50%, and 75% 'randomly' selected reads)
Could you please explain the procedure or provide the command used?
Thanks
Najeeb ...
written 8 months ago by
always_learning • 1000
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... I think "genotype get set to unknown" will be a better approach. What do you think? ...
written 9 months ago by
always_learning • 1000
0
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... I can't run this again. This is merged VCF of around 6000 samples. I think It will fine to remove such sites from VCF. ...
written 9 months ago by
always_learning • 1000
2
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1
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409
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... I have few SNP with ploidy > 2 in my VCF(Human) generated by GATK with genotypes like "0/1/1". Any idea how I can remove them from my VCF file? Any tools that do that? ...
written 9 months ago by
always_learning • 1000
• updated
7 months ago by
tpoterba • 50
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... Thanks !! But I have just frequencies !! So I don't think that I can do similar to that. ...
written 13 months ago by
always_learning • 1000
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... Please find dropbox link for example data.
https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0 ...
written 13 months ago by
always_learning • 1000
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