User: sutturka

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sutturka170
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USA
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10 hours ago
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6 years, 6 months ago
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Posts by sutturka

<prev • 31 results • page 1 of 4 • next >
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Comment: C: cnvkit bgzf_read error 4 after 4 bytes
... I am also facing similar issue, I get error/warning as: [E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes [E::bgzf_uncompress] Inflate operation f ...
written 25 days ago by sutturka170
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Comment: C: Y axis PlotHeatMap Deeptools
... This explanation helps. I have additional question: **What does negative scale imply on profile plot? I am plotting RNASeq data in two ways:** - Separate BAMs for control and treatment - After BAMcompare i.e. after normalizing the treatment against control. [See image here.](https://app.box.c ...
written 3 months ago by sutturka170
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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 7 months 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 16 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 17 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 23 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 23 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 2.1 years 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 2.2 years 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 2.2 years ago by sutturka170

Latest awards to sutturka

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Student 16 months ago, asked a question with at least 3 up-votes. For Concept of Matched normal vs. Virtual Normal
Popular Question 19 months ago, created a question with more than 1,000 views. For Concept of Matched normal vs. Virtual Normal
Scholar 3.3 years ago, created an answer that has been accepted. For A: Career in Bioinformatics
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Scholar 3.5 years ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics

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