User: Jackie

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Jackie50
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Posts by Jackie

<prev • 35 results • page 1 of 4 • next >
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Comment: A: Does Cufflinks report chimeric transcripts/fusion genes?
... Hi Ron, thanks for the input. We do use STAR for calling fusions, but we also want to find out the coverage/FPKM at the fusion breakends. Since Cufflinks is the tool we use in our pipeline for calculating FPKMs, we wonder whether Cufflinks can report the fusion transcripts (we thought that could be ...
written 14 hours ago by Jackie50
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Comment: A: Does Cufflinks report chimeric transcripts/fusion genes?
... Can anyone please help with this question? Thanks a lot! ...
written 16 hours ago by Jackie50
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Does Cufflinks report chimeric transcripts/fusion genes?
... I understand that Cufflinks can report FPKM on novel transcripts (different isoforms) if using proper parameters, but I wonder whether cufflinks is able to report FPKM on chimeric transcripts/gene fusions between different genes? for example, if a fusion happens between exon1 of gene1 and exon5-6 of ...
cufflinks chimeric transcripts fusions written 21 hours ago by Jackie50
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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 5 months ago by Jackie50
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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 6 months ago by Jackie50
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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 6 months ago by Jackie50
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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 6 months ago by Jackie50 • updated 6 months ago by Alex Reynolds22k
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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 10 months ago by Jackie50
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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 10 months ago by Jackie50
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Comment: A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 11 months ago by Jackie50

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
Popular Question 13 months ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

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