User: gsr9999

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gsr999960
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Posts by gsr9999

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... Thanks for this summary list ...
written 28 days ago by gsr999960
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Answer: A: How to generate a .sam/.bam file of a particular chromosome or even a particular
... You can also use sambamba tool to slice the existing bam to specific regions. It is much faster than samtools. Example : $sambamba slice -o my_output_bam_file.bam Input_bam_file.bam chr1:100-200 Or you can extract reads for an entire chromosome by just specifying the chromosome name in option Exa ...
written 9 weeks ago by gsr999960
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Comment: C: question about API for SNPs
... thanks for this info on Ensemble Restful apis ...
written 3 months ago by gsr999960
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Comment: C: Searching for ClinVar entries based on SNP annotation
... thanks for the post and link ...
written 3 months ago by gsr999960
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how to Automate the Retrieval of Variant-related Information from Pubmed, dbSNP, ClinVar, HGMD etc
... Dear Biostar leaders, I have started to work on a new Variant Re-Classification project in my lab, and I am wondering how others implement this and it would be great if you could share/advice on best approaches being practiced. After sanger confirmation of WES variants, we classify variants based o ...
genome gene next-gen snp written 3 months ago by gsr999960 • updated 3 months ago by Kevin Blighe21k
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Comment: C: Can Breakdancer be applied on Paired end Exome Sequencing data for germline copy
... Hi Cameron, Thank you for the details/information on how breakdancer is best suited for short read sequencing <2*50 bp. Thank u for pointing me to other tools like lumpy, manta and gridss. ...
written 3 months ago by gsr999960
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Answer: A: Can Breakdancer be applied on Paired end Exome Sequencing data for germline copy
... After reading review papers, I learnt that CNV detection in Exome data by SV detection tools that are based on Discordant Read Pairs like Breakdancer may not be able to detect CNVs in every case. These tools require at least one breakpoint to be in exonic regions, and when real breakpoint is outside ...
written 3 months ago by gsr999960
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Comment: C: Recommendations for CNV calling algorithms/programs to benchmark
... Can Breakdancer be applied on Paired End Whole Exome sequencing data ? ...
written 3 months ago by gsr999960
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Can Breakdancer be applied on Paired end Exome Sequencing data for germline copy number/sv detection?
... Dear Biostar Leaders, We have a Paired End Sequencing Reads from Whole Exome Sequencing run generated on a cell line that is known to contain 15kb deletion on chrX. This 15kb region includes part of exon 4 of MECP2 gene. I have run Pindel and DELLY tools on it and this 15kb deletion is successfully ...
genome next-gen written 3 months ago by gsr999960 • updated 3 months ago by d-cameron1.8k
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Comment: A: Impact on NGS workflows - due to Vulnerabilities - Meltdown and Spectre ?
... @genomax, thank you for your answer ...
written 4 months ago by gsr999960

Latest awards to gsr9999

Popular Question 14 months ago, created a question with more than 1,000 views. For BWA MEM 0.7.12 Error : [gzread] : invalid distance code
Scholar 15 months ago, created an answer that has been accepted. For A: Gcat Benchmarking Tool For Comparison Of Genome Analysis Software
Scholar 15 months ago, created an answer that has been accepted. For A: Gcat Benchmarking Tool For Comparison Of Genome Analysis Software

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