User: Jackie

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Jackie40
Reputation:
40
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New User
Location:
United States
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1 month, 2 weeks ago
Joined:
5 years, 4 months ago
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Posts by Jackie

<prev • 32 results • page 1 of 4 • next >
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How to download all the VCFs generated from WXS BAM in TCGA legacy archive?
... 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 ...
wxs tcga vcfs written 6 weeks ago by Jackie40
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... 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 Jackie40
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... 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 Jackie40
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How to extract all the simple repeats from the hg19 reference genome
... 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 ...
simple repeats reference genome written 9 weeks ago by Jackie40 • updated 9 weeks ago by Alex Reynolds21k
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benchmarking/validation tools for CNVs
... 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! ...
truth set benchmarking cnv validation written 5 months ago by Jackie40
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CNV tools for hybridization vs. amplicon capture WES data
... 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 ...
amplicon cnv hybridization bioinformatics tools written 6 months ago by Jackie40
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Comment: A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 7 months ago by Jackie40
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GT tag in VCF spec
... 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 ...
vcf gt tags valid written 7 months ago by Jackie40
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What does 'frac' mean in cufflinks output transcripts.gtf
... 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 ...
fpkm cufflinkts frac written 7 months ago by Jackie40
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How to output a pdf with both tables and plots using perl
... 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 ...
perl histogram pdf:table plot written 8 months ago by Jackie40 • updated 8 months ago by shenwei3563.4k

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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