User: Sharon

gravatar for Sharon
Sharon250
Reputation:
250
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Trusted
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Last seen:
9 hours ago
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9 months, 1 week ago
Email:
s***********@gmail.com

Posts by Sharon

<prev • 183 results • page 1 of 19 • next >
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Comment: C: Variant with AD 14,3 is heterozygote?
... Great, got it now. Thanks so much for the clear explanation. Much appreciated Gabriel :) ...
written 2 days ago by Sharon250
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Comment: C: Variant with AD 14,3 is heterozygote?
... Interesting figure. Never thought about this. So I check if the reads are mappable, if yes, that's a sign of less likely for errors, which means trust the call and trust the variant? Do I understand right? ...
written 2 days ago by Sharon250
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Comment: C: Variant with AD 14,3 is heterozygote?
... Thanks Gabriel for the nice answer. I did not use a nor b, I will give them a try. Just used GATK pipeline. Thanks dariober, that's another good point I did not think of, I will check other reads . Thanks ...
written 2 days ago by Sharon250
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Variant with AD 14,3 is heterozygote?
... **Hi everyone** I would like to take a second opinion regarding a variant with DP =17. The variant is in a very high GC content area so the low coverage is reasonable. I do hard filtering because I have few samples for VQSR, I thinks it is okay according to GATK hard filtering, the values are as ...
exome vcf written 2 days ago by Sharon250 • updated 2 days ago by Gabriel R.2.4k
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Comment: C: cufflinks missing some annotations?
... Hi Fabio Thanks. I am using lncscore, it is a tool for lncRNA. it takes assembled transcripts in fasta format, so I convert my transcricpts.gtf to fasta using cufflinks gffread tool to input the transcripts.fa to lncscore. But when the original transcript.gtf has "Cuff" id instead of a gene id ...
written 4 days ago by Sharon250
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cufflinks missing some annotations?
... Hi Every one Why I am having some annotations missing in cufflinks -g option chr1 Cufflinks transcript 679399 679585 1000 . . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "12.3670741574"; frac "1.000000"; conf_lo "5.199859"; conf_hi "19.534289"; cov "90.723 ...
gtf rna-seq transcripts written 4 days ago by Sharon250
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Annovar for mouse buildver and downdb?
... Hi All I am trying to use annovar for mosue data. I used this command to create the mouseDB: perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mousedb/ And it works fine and got he refgene db for mouse. Now, I need to build the rest of annotation fields. something ...
vcf annovar written 5 days ago by Sharon250
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Comment: C: Builiding reference for annovar based on build37.1?
... I will try that conversion. Thanks a lot igor. ...
written 8 days ago by Sharon250
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Comment: C: Builiding reference for annovar based on build37.1?
... -webfrom allows from URL too as the documentation . But if I download it, how can I use what I downloaded in the command? ...
written 8 days ago by Sharon250
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Builiding reference for annovar based on build37.1?
... Hi Everyone Have anyone used `annotation_variation.pl` by Annovar to build a reference from NCBI build 37.1. I need this version exactly to annotate some old versions data. When I use UCSC hg19, the annotations makes less sense I think. perl annotate_variation.pl -buildver b37 -downdb \ ...
annovar build37.1 written 8 days ago by Sharon250 • updated 8 days ago by igor5.7k

Latest awards to Sharon

Voter 6 weeks ago, voted more than 100 times.
Scholar 4 months ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Centurion 4 months ago, created 100 posts.
Scholar 4 months ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 4 months ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 5 months ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 5 months ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Supporter 5 months ago, voted at least 25 times.

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