User: poisonAlien

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Cancer genomics

Posts by poisonAlien

<prev • 278 results • page 1 of 28 • next >
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Comment: C: Generate phylogenetic tree from primary and metastatic tumors
... your 8 samples, are they from same patient ? i.e, multi region sequencing ? ...
written 10 hours ago by poisonAlien2.3k
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Answer: A: Generate phylogenetic tree from primary and metastatic tumors
... 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 poisonAlien2.3k
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Answer: A: Broad rules of thumb on # of variations
... 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 poisonAlien2.3k
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Answer: A: How to annotate only selected genes on a heatmap
... [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 poisonAlien2.3k
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Comment: C: all the peaks of MACS2 BED file starting at position 0
... 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 poisonAlien2.3k
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Comment: C: Which peaks in the bed file output by MACS2 are significant ?
... 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 poisonAlien2.3k
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Comment: C: Which peaks in the bed file output by MACS2 are significant ?
... 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 poisonAlien2.3k
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Comment: C: Calculate Variant Allele Frequency in a TCGA dataset
... +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 poisonAlien2.3k
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Comment: C: Are there NGS-based CNV callers that utilise allele frequency?
... [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 poisonAlien2.3k
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Comment: C: How to understand somatic mutation of ICGC data
... 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 poisonAlien2.3k

Latest awards to poisonAlien

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Popular Question 3 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 4 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 4 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 4 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 5 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 5 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar 5 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 9 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 10 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 12 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Scholar 12 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP

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