User: sutturka

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sutturka120
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120
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USA
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4 days, 10 hours ago
Joined:
4 years, 3 months ago
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Posts by sutturka

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
... Please check my answer in [this thread][1]. It might be useful. [1]: https://www.biostars.org/p/264524/#300448 ...
written 3 months ago by sutturka120
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Answer: A: Experiences with large datasets
... Please check my experience with SRA download [here][1]. It might be useful. [1]: https://www.biostars.org/p/264524/#300448 ...
written 3 months ago by sutturka120
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Answer: A: Download SAM/BAM files from SRA takes ages!!!
... I would like to share my twist and turns with SRA download. It took several interactions with NCBI staff to figure this out. below are the steps: **Prerequisite:** sra-toolkit and aspera plugin installed. The instructions are specific to Linux environment. **Steps:** 1. Configure workspace Th ...
written 3 months ago by sutturka120
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Answer: A: How to use GNU parallel to download SRA files
... There is a [parallel-fastq-dump][1] utility available which might be useful. I am yet to test the performance and update the answer soon. [1]: https://github.com/rvalieris/parallel-fastq-dump ...
written 4 months ago by sutturka120
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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 8 months ago by sutturka120
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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 8 months ago by sutturka120
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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 months ago by sutturka120 • updated 8 months 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 12 months ago by sutturka120
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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 12 months ago by sutturka120
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Comment: C: Career in Bioinformatics
... I second "Masters in bioinformatics" suggestion considering your expertise in programming. ...
written 15 months ago by sutturka120

Latest awards to sutturka

Scholar 12 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics
Scholar 15 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics

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