User: sutturka

gravatar for sutturka
sutturka110
Reputation:
110
Status:
Trusted
Location:
USA
Last seen:
1 day ago
Joined:
3 years, 11 months ago
Email:
s************@gmail.com

about me

Posts by sutturka

<prev • 11 results • page 1 of 2 • next >
0
votes
2
answers
198
views
2
answers
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 10 days ago by sutturka110
0
votes
1
answer
501
views
1
answers
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 4 months ago by sutturka110
0
votes
1
answer
293
views
1
answers
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 4 months ago by sutturka110
5
votes
1
answer
293
views
5 follow
1
answer
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 4 months ago by sutturka110 • updated 4 months ago by Chris Miller19k
3
votes
2
answers
511
views
2
answers
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 8 months ago by sutturka110
1
vote
2
answers
1.3k
views
2
answers
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 8 months ago by sutturka110
1
vote
1
answer
640
views
1
answers
Comment: C: Career in Bioinformatics
... I second "Masters in bioinformatics" suggestion considering your expertise in programming. ...
written 11 months ago by sutturka110
4
votes
1
answer
640
views
1
answers
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 11 months ago by sutturka110
0
votes
2
answers
1.4k
views
2
answers
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 13 months ago by sutturka110
0
votes
6
answers
24k
views
6
answers
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 16 months ago by sutturka110

Latest awards to sutturka

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
Scholar 11 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1808 users visited in the last hour