User: sutturka

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sutturka100
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100
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Location:
USA
Last seen:
2 days, 13 hours ago
Joined:
3 years, 8 months ago
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Posts by sutturka

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Clusterprofiler for KEGG enrichment (non-model species)
... May be [this document][1] will be useful. [1]: http://www.bioconductor.org/packages//2.10/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler_for_unsupported_organism.pdf ...
written 6 weeks ago by sutturka100
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Comment: C: Concept of Matched normal vs. Virtual Normal
... Thank you Chris Miller for the suggestions. I have related question about sample collection strategy. 1. For WGS, is it sufficient to collect samples from any somatic tissues? i.e. may be lymphoma tumor samples and normals from the skin/blood of the same patient rather than the tissue adjacent to ...
written 7 weeks ago by sutturka100
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Concept of Matched normal vs. Virtual Normal
... I have a question about the **matched normal sample vs virtual normal sample**. By definition, a matched normal (MN) is a sample of healthy tissue of the same individual, in order to distinguish germline mutations from somatic mutations. On the other hand, samples from healthy, unrelated individuals ...
virtual normal somatic mutations matched normal written 8 weeks ago by sutturka100 • updated 8 weeks ago by Chris Miller19k
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Answer: A: Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
... The tools [Pilon][1] and [Icorn2][2] performs assembly polishing with Illumina data. I am not sure if Icorn2 also takes PacBio reads for correction. Running additional rounds of Quiver may be the helpful to use the PacBio reads efficiently. [1]: http://software.broadinstitute.org/software/pilon/ ...
written 5 months ago by sutturka100
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Answer: A: SSPACE assembling Genome!
... I am sharing my experience with SSPACE as it may be useful for someone. **Data:** We have multiple Paired-end and mate-pair libraries from a large eukaryotic genome. We performed assembly through ABySS and ran SSPACE on ABySS contigs to perform scaffolding and contig extension. **Issue:** SSPACE ...
written 5 months ago by sutturka100
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Comment: C: Career in Bioinformatics
... I second "Masters in bioinformatics" suggestion considering your expertise in programming. ...
written 8 months ago by sutturka100
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Answer: A: Career in Bioinformatics
... +1 for first completing your four years degree before seeking programs abroad. I agree that there are limited bioinformatics opportunities in India, especially related to research. But if you have good coding skills, then you can think about joining an IT company (several of them work on biological ...
written 8 months ago by sutturka100
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Comment: C: How basemean/basemeanA/basemeanB and log2foldchange are counted in DESeq2 ?
... This is really very helpful information. Can you please suggest how to calculate the log2fc or fc using the values from mcols(dds) output. I calculated first and second basemean as suggested and log2fc by log(basemean2/basemean1). However, it does not match with DeSeq2 output value. 1. MLE_Interce ...
written 10 months ago by sutturka100
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Answer: A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
... Try bedtools getfasta : http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 13 months ago by sutturka100
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Answer: A: Masurca Error With Illumina Assembly
... Hi, I contacted developers regarding this and they suggested that read_names does not matter during pre-processing of data. He suggested me to perform a test with my fastq file: > file -b -i jumps.A.fastq This gave me the results like: text/x-python; charset=us-ascii I emailed results t ...
written 3.7 years ago by sutturka100

Latest awards to sutturka

Scholar 5 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics
Scholar 8 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics

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