User: rse

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rse70
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Posts by rse

<prev • 77 results • page 1 of 8 • next >
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Comment: C: Structural Variations in IGV and SV Callers
... Thanks for the reply. Maybe the third snapshot can be a false positive. Are the first 2 screenshots hinting towards deletion? I would presume a dip in coverage or no coverage in a region to be called a deletion. I read IGV manual, but it doesn't tell about structural variation so well. Can you tell ...
written 25 minutes ago by rse70
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Comment: C: Structural Variations in IGV and SV Callers
... Thanks for your reply. The SV Calls and the snapshot is attached. Thanks SV Calls: 1 5175945 MantaDEL:378:1:2:0:0:0 A . . END=81713905;SVTYPE=DEL;SVLEN=-76537960;IMPRECISE;CIPOS=-195,196;CIEND=-340,341;UPSTREAM_PAIR_COUNT=5;DOWNSTREAM_PAIR_COUNT=6;PAIR_COUNT=5 1 725923 MantaDEL:11:21 ...
written 23 hours ago by rse70 • updated 23 hours ago by ATpoint8.0k
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Structural Variations in IGV and SV Callers
... Hello, I performed SV Calling using 3 SV Callers and all of the SV Callers showed a deletion at a particular genomic location. But i when i view the same genomic location in IGV, i see that all the whole region is well covered and there is no decline in the coverage from the neighbouring locations ( ...
sequencing written 23 hours ago by rse70
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Comment: C: loaded a sorted bam file in IGV but I can't see anything
... Zoom in to the maximum perhaps ...
written 11 days ago by rse70
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Comment: C: Gold standard variant set
... Yes, i have sequenced my sample and want to compare pipelines. Thank you for suggesting this reference paper. Is there any more studies describing the process of generating a gold standard dataset for our sample? Thanks ...
written 11 days ago by rse70
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Answer: A: Find chromosome number
... You can perform NCBI-BLAST or do UCSC BLAT ...
written 12 days ago by rse70
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Gold standard variant set
... Hi, I want to compare different variant calling pipelines for an exome sample. But, I don't know what gold standard to use for evaluation of performance parameters (sensitivity, specificity, etc). Can anyone suggest me how to create a gold standard for my exome. The genome in a bottle contain gold ...
genome next-gen sequencing written 14 days ago by rse70
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Comment: C: Adding bam file (Any file) as URL
... Sure, i will try it out. Thanks :) ...
written 6 weeks ago by rse70
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Comment: C: Adding bam file (Any file) as URL
... Sure, thanks :) I will probably extract that regions from bam file and make smaller bam files ...
written 6 weeks ago by rse70
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Comment: C: Adding bam file (Any file) as URL
... Thanks. I have tried IGV :) ...
written 6 weeks ago by rse70

Latest awards to rse

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Learn to develop bioinformatics tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Learn to develop bioinformatics tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Retrieving gene names from list of mRNA accession IDs
Scholar 6 months ago, created an answer that has been accepted. For A: What is Read Group platform??

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