User: Jackie

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Jackie60
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Posts by Jackie

<prev • 38 results • page 1 of 4 • next >
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Comment: C: How to create dummy VCF with fusion variants
... Sorry about the confusion, and thanks for providing the hyperlink. I have updated the post by inserting the hyperlink for Mitelman. ...
written 12 weeks ago by Jackie60
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Comment: C: How to create dummy VCF with fusion variants
... Thank you Pierre for the answer. I have actually already downloaded the raw data from Mitelman website, but the question now is, how to convert the breakpoints in cytoband format into genomics coordinates, as that's what would be needed for generating a VCF. I think I can download some cytoband ann ...
written 12 weeks ago by Jackie60
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How to create dummy VCF with fusion variants
... I am developing a tool which would take a gene list as input, and the output would be a VCF including fusion variants involving the genes of interest. I am going to use [Mitelman database][1] which has a comprehensive curation of fusions from published literatures. However, the breakpoints are in ...
fusion databases mitelman fusions written 12 weeks ago by Jackie60 • updated 12 weeks ago by d-cameron1.8k
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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 4 months ago by Jackie60
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Comment: A: Does Cufflinks report chimeric transcripts/fusion genes?
... Can anyone please help with this question? Thanks a lot! ...
written 4 months ago by Jackie60
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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 4 months ago by Jackie60
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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 9 months ago by Jackie60
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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 10 months ago by Jackie60
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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 10 months ago by Jackie60
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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 10 months ago by Jackie60 • updated 10 months ago by Alex Reynolds24k

Latest awards to Jackie

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
Popular Question 17 months ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

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