User: sutturka

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sutturka170
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USA
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1 week, 2 days ago
Joined:
6 years ago
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Posts by sutturka

<prev • 29 results • page 1 of 3 • next >
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Answer: A: Noisy germline CNV data using CNVKit
... [This link][1] will answer you question regarding the grey and orange bars on the scatter plot. Search through Github issues and you may get more answers. [1]: https://github.com/etal/cnvkit/issues/286 ...
written 6 weeks ago by sutturka170
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Comment: C: Dotplot for filtered pathways result
... Great. Can you please add snippet of **S1.csv** file for reference? ...
written 10 months ago by sutturka170
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Answer: A: Downstream analysis of VCF files obtained from VarScan2
... It may be better to convert VCF to MAF format (We do this for somatic variants only) using the [vcf2maf][1] utility. Once in MAF format, to merge the patients data together, you can simply `cat` the files together and patient identity is maintained in a separate column. Combined MAF file can be anal ...
written 11 months ago by sutturka170
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Comment: C: featureCounts in predicting strand specificity
... Hi vrehaman, I am in a similar situation like you. I see the issue is with strands setting where featurecounts with `-s 1` and `-s 2` gave similar number of reads while I get double the number of reads assigned with `-s 0`. With RSeQC, I see most reads fraction (>90%) assigned to strand ``` Fra ...
written 17 months ago by sutturka170
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Did you get this resolved by using specific parameters? I also see that you are changing the `--shift` option which is recommended to keep as 0 with format BAMPE. See MACS options. How did you determined the `--extsize` to 54? ...
written 17 months ago by sutturka170
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Comment: C: Running vcf2maf on snpeff-annotated vcfs
... [This issue][1] on github page is very similar and comments on this issue may be helpful. [1]: https://github.com/mskcc/vcf2maf/issues/174 ...
written 19 months ago by sutturka170
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Answer: A: Issue converting VCF to MAF using snpEff annotations
... Hi, Please check the [GitHub issues][1] page which have solution for using this tool without installing VEP or use SnpEff annotated files. [1]: https://github.com/mskcc/vcf2maf/issues/160 ...
written 20 months ago by sutturka170
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Answer: A: Running vcf2maf on snpeff-annotated vcfs
... This is a known issue and could happen because of newer annotation types added in SnpEff. Please see the [GitHub issues][1] page for vcf2maf. [1]: https://github.com/mskcc/vcf2maf/issues?utf8=%E2%9C%93&q=Use%20of%20uninitialized%20value ...
written 20 months ago by sutturka170
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Comment: C: Convert (Copy Number Variation) CNV to gene
... Let me jump in and point you to [this discussion][1]. If you have confident CNV calls then you can use bedtools to get genes overlapping with CNV segments. Let's say I am fairly confident about the CNV calls. However, I am not sure if mere overlap of genes with CNV segments is enough to assign genes ...
written 20 months ago by sutturka170
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Comment: C: How to annotate CNV events with gene information?
... I was able to follow this approach and get the annotations for the CNVs. Essentially, I got the genes which are overlapping with CNVs and then I assigned the status (Amp/Del/Neutral) to each gene according to CNV status. However, this is a mere overlap approach and what is your opinion on directly u ...
written 20 months ago by sutturka170

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