User: poisonAlien
poisonAlien • 2.3k
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Cancer genomics
Posts by poisonAlien
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... your 8 samples, are they from same patient ? i.e, multi region sequencing ? ...
written 10 hours ago by
poisonAlien • 2.3k
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... There are quite a few programs available. [Lichee][1] does better job. It also incorporates allele frequencies rather than using just a binary matrix.
[1]: https://github.com/viq854/lichee ...
written 1 day ago by
poisonAlien • 2.3k
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... It depends, if your WGS vcf file is unfiltered and contains all raw variants, you would expect at-least over 2 million variants. But if it has already been filtered to contain only variants within coding part of the genome, number of variants should be equal to that of WXS.
Regarding WXS, it again ...
written 1 day ago by
poisonAlien • 2.3k
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... [ComplexHeatmap][1] can do this. I believe article uses the same.
[1]: http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html#toc_14 ...
written 3 days ago by
poisonAlien • 2.3k
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... why is your p-value cut-off set at 24 ? macs2 command, shouldn't it be `macs2 callpeak` ? Is there any particular reason your alignment files are in SAM format ? (BAM is better, compressed and binary so it won't get messed up, unlike SAM which is just a text file) ...
written 6 days ago by
poisonAlien • 2.3k
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... MACS2 output always contains .narrowPeak file except If you had run MACS2 with `--broad` argument, where it will generate broadPeak and gappedPeak file. Maybe check your output directory again ? ...
written 10 days ago by
poisonAlien • 2.3k
1
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... AFAIK, [narrowPeak][1] file generated by MACS2 conatins all peaks below threshold (q<0.05, 9th column) and you can directly use this file with annotatePeaks, without needing to cut 1st three columns, also try loading narrowpeak file into IGV.
[1]: https://genome.ucsc.edu/FAQ/FAQformat.html#f ...
written 10 days ago by
poisonAlien • 2.3k
0
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1
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107
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1
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... +1 for mentioning - "fraction of individuals with a mutation in a population."
VAF could be an ambiguous term without proper context. ...
written 17 days ago by
poisonAlien • 2.3k
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... [Sequenza][1] uses BAF. I think [cnMops][2] does too.
[1]: https://www.ncbi.nlm.nih.gov/pubmed/25319062
[2]: https://academic.oup.com/nar/article/40/9/e69/1136601/cn-MOPS-mixture-of-Poissons-for-discovering-copy ...
written 27 days ago by
poisonAlien • 2.3k
0
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... This is because 5 transcripts are affected by mutation MU28652212. You need to prioritize a transcript out of 5. One way to do this is use [maf2maf][1] which will do this for you. You can use [mafttols][2] to convert ICGC simple somatic mutation format to MAF and further process them (apologies for ...
written 28 days ago by
poisonAlien • 2.3k
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For questions on rna-seq data analysis
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For A: Is there any better method to find significant SNVs ?
Scholar
10 months ago,
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For A: Is there a good manual/tutorial for TreeView?
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