User: rse

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rse30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 days, 22 hours ago
Joined:
3 years, 6 months ago
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Posts by rse

<prev • 49 results • page 1 of 5 • next >
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Answer: A: No coverage or very low coverage in the Complete Genomics data
... I’m sorry, I didn’t explain the issue properly. I’m working on CG WGS data with avg read depth of 40x. The QC metrics looks good for all parameters and the alignment rate is 97.43%. However, I had used cgaTools to convert tsv files provided by CG to BAM. When I visualize these BAM files on IGV, I se ...
written 13 days ago by rse30
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Answer: A: Visualization software for large variations
... Ok, will try. Thank you ...
written 18 days ago by rse30
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Comment: C: No coverage or very low coverage in the Complete Genomics data
... Thank you for your reply. We are pretty sure that the source and quality of DNA was good. The alignment % was around 97%. Will look into the QC meterics ...
written 20 days ago by rse30
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No coverage or very low coverage in the Complete Genomics data
... Hi, Has anyone worked on Complete Genomics data? Most of the exons in the data have no coverage or very low coverage (5-10 reads only) even though the reads are sequenced at 40X coverage. Can anyone explain why is it so? Thanks Regards ...
next-gen sequencing written 21 days ago by rse30
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Comment: C: IGV Visualization Insert Size
... Thank you for your reply, but i am still unclear whether the insert refers to the unsequenced DNA segment b/w the 2 reads? ...
written 26 days ago by rse30
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IGV Visualization Insert Size
... Hi, I am visualizing alignments using IGV. I want to ask what do you mean by Insert? Is insert size a large unsequenced segment sitting right in between the two reads which escapes sequencing and also shearing during library prep stage? How to validate the existence of a large insert such as 3Mb o ...
next-gen alignment sequencing written 26 days ago by rse30
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Comment: A: Visualization software for large variations
... Thanks, but i have to do from alignment data (.bam files) ...
written 27 days ago by rse30
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Visualization software for large variations
... Hi, Is there good visualization software for large variations? I am aware of IGV but i am having difficulty in estimating the large variations. Also what is insert size and how does it correlate to the size of the deletion/insertion? Thanks ...
alignment next-gen sequencing written 27 days ago by rse30
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(Closed) IGV Visualization Insert Size
... Hi, I have a question regarding visualization of the large structural variations through IGV. I am visualizing large variations for a case. I observe dark red, blue and green reads which denotes deletion, insertion and duplication respectively according to the IGV manual. The reads have a insert ...
alignment next-gen sequencing written 4 weeks ago by rse30 • updated 24 days ago by Kevin Blighe11k
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Answer: A: Loss of heterozygosity analysis from SNV files
... Thank you Yes, VarScan2 outputs LOH events from tumor-normal pair, but these are SNVs only. And since LOH is a region of allelic imbalance. How to get the region of LOH from these SNP-Indels? ...
written 9 months ago by rse30

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