User: Sharon
Sharon • 250
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Posts by Sharon
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... Great, got it now. Thanks so much for the clear explanation. Much appreciated Gabriel :) ...
written 2 days ago by
Sharon • 250
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... 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
Sharon • 250
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... 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
Sharon • 250
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... **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 ...
written 2 days ago by
Sharon • 250
• updated
2 days ago by
Gabriel R. • 2.4k
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... 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
Sharon • 250
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... 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 ...
written 4 days ago by
Sharon • 250
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... 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 ...
written 5 days ago by
Sharon • 250
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... I will try that conversion. Thanks a lot igor. ...
written 8 days ago by
Sharon • 250
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... -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
Sharon • 250
0
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... 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 \
...
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
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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
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