User: Jackie
Jackie • 40
- Reputation:
- 40
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- New User
- Location:
- United States
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 5 years, 4 months ago
- Email:
- d*******@gmail.com
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Posts by Jackie
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... How to download all the VCFs associated with the WXS BAM files?
In the legacy archive in GDC portal, if you select 'WXS' under 'Experimental Strategy', only BAM files are kept (e.g., no VCFs ). Usually, there are two BAM files labelled as 'WXS', one should be the tumor sample, the other should be th ...
written 6 weeks ago by
Jackie • 40
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... Thank you, Alex, that's a great resource, and I have downloaded the repeat masker (RM) file, I think combining the list generated using Pierre's code with this file will give a good starting list.
However, I am still trying to understand why, even this RM file is missing some simple repeats, e.g., ...
written 9 weeks ago by
Jackie • 40
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... Thank you so much for posting the C program. It seems to work perfect, but I have another question. Does this program find only mono- repeats or any repeats with total len >5bp?
...
written 9 weeks ago by
Jackie • 40
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5 follow
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... I am trying to get a comprehensive list of simple repeats (mono-, di-, tri-, tetra-) in the human genome (hg19). I have downloaded the [simpleRepeat.txt.gz][1] from UCSC, but seems it is missing some of the repeats we are interested in. For example, chr1:981861-981868[CCCCCCCC], chr1:1116223-111623 ...
written 9 weeks ago by
Jackie • 40
• updated
9 weeks ago by
Alex Reynolds ♦ 21k
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... Are there good benchmarking/validation tools for CNVs?
By 'benchmarking/validation', I mean, you feed the tool a truth set and the CNVs called by a CNV caller, then the tool will output something like the sensitivity and specificity of the CNV caller.
Thanks! ...
written 5 months ago by
Jackie • 40
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... In this review paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1), it lists several tools that are suitable for CNV detection with WES data (e.g., Control-FREEC, CoNIFER, XHMM, ExomeCNV, CONTRA), but it does not mention whether these tools work well with the hy ...
written 6 months ago by
Jackie • 40
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Comment:
A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 7 months ago by
Jackie • 40
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... Hi,
Is GT tag in the FORMAT col a required tag by VCF spec? If a VCF does not have GT tag, is it still a valid VCF? Or put it another way, what is the minimum information that makes a VCF valid?
Thanks ...
written 7 months ago by
Jackie • 40
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... In Cufflinks output transcripts.gtf, there is a field called 'frac'. What does that mean?
chr1 Cufflinks transcript 18957500 19062632 361 + . gene_id "PAX7"; transcript_id "NM_002584.2"; FPKM "218.4530519923"; frac "0.219171"; conf_lo "200.428676"; conf_h ...
written 7 months ago by
Jackie • 40
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... Hi,
I am using perl PDF:Table module to generate a pdf file.
In the PDF, there will be 4 sections, 1st, 2nd, and 4th sections are all tables, and the 3rd section needs to be a histogram.
Can someone advise how can this be done? I know how to make a PDF with all the sections being tables, but not ...
written 8 months ago by
Jackie • 40
• updated
8 months ago by
shenwei356 • 3.4k
Latest awards to Jackie
Popular Question
5 months ago,
created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
Popular Question
9 months ago,
created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
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