User: Tania

gravatar for Tania
Tania120
Reputation:
120
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Last seen:
15 hours ago
Joined:
6 months, 2 weeks ago
Email:
f**************@gmail.com

Posts by Tania

<prev • 121 results • page 1 of 13 • next >
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Comment: C: Coverage in whole genome sequencing
... Thanks Sharon and Kevin a lot. I will try that ! ...
written 15 hours ago by Tania120
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Comment: C: Coverage in whole genome sequencing
... Yes, I read this kevin, thank you :) I just want to understand more what uncertain mean. Like there is no reads covering this region at all, or there are reads but low confidence. Like uncertain is too open to know what is going on here. The reason is I am checking a varaint. it is found in the e ...
written 17 hours ago by Tania120
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Comment: C: Coverage in whole genome sequencing
... I think yes. It is old data in the lab, have to post-process and just have the output files from cgatools. ...
written 19 hours ago by Tania120
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Coverage in whole genome sequencing
... Hi everyone If a range of positions is annotated as **no-call** in whole genome ` ` in `cgatools` output files. I am interested in a varaint in this region that doesn't show up in the variants file and I need to check the coverage. Does no-call means no reads here. I read the definition in cgat ...
wgs coverage written 20 hours ago by Tania120 • updated 15 hours ago by Sharon310
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Comment: C: Mappability in duplicate gene?
... From IGV, I got the read length, say 150 and my variant is in the middle for example. then I checked the position of this gene by considering around 200 bases around my variant (I mean including the read length) in this window. I looked for Duke Unique_35 mappability in the UCSC. No command line. ...
written 8 days ago by Tania120
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Mappability in duplicate gene?
... Hi Every one I am checking an interesting variant in a duplicate gene. I am checking mappability of the region, I get the Duke Unique_35 mappability from the UCSC genome browser. I took a window size greater than my read length and found the mappability is 1. Does this make sense given the gene ...
variant calling exome sequencing written 9 days ago by Tania120
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Comment: C: add gene names in bed file
... human genome hg19 :) Thanks. it works now, I needed to convert my own transcripts to bed. ...
written 9 days ago by Tania120
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Comment: C: add gene names in bed file
... Thank you cpad0112 and EagleEye, I will give this a try :) ...
written 22 days ago by Tania120
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add gene names in bed file
... Hi Everyone I converted the gtf file I got from stringtie to bed. The bed still contains the stringtie gene and transcripts code (same thing if I used cufflinks instead) , is there a way to post-process this bed file to have real gene names and transcripts not stringtie nor cufflinks ids: ch ...
bed annotations written 22 days ago by Tania120 • updated 22 days ago by Alex Reynolds23k
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Comment: C: How low is OK to accept variants in high/low GC content regions?
... Not me, my advisor, and this is when Kevin mentioned patient care, I said I am checking the logic behind my analysis and he cab decide whatever he think with his patients :) Actually, this is my role, I discuss with my advisor my bioinformatics logic, and never think about this patient care stuff, ...
written 24 days ago by Tania120

Latest awards to Tania

Centurion 10 weeks ago, created 100 posts.
Student 10 weeks ago, asked a question with at least 3 up-votes. For Is there a better tool for visualizing your variants after annotation than Excel?
Supporter 5 months ago, voted at least 25 times.
Rising Star 5 months ago, created 50 posts within first three months of joining.

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