User: Jackie
Jackie • 70
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Posts by Jackie
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... Sorry about the confusion, and thanks for providing the hyperlink.
I have updated the post by inserting the hyperlink for Mitelman. ...
written 2.4 years ago by
Jackie • 70
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... 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 2.4 years ago by
Jackie • 70
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... 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 ...
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... 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 2.5 years ago by
Jackie • 70
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... Can anyone please help with this question?
Thanks a lot! ...
written 2.5 years ago by
Jackie • 70
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... 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 ...
written 2.5 years ago by
Jackie • 70
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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 2.9 years ago by
Jackie • 70
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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 3.0 years ago by
Jackie • 70
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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 3.0 years ago by
Jackie • 70
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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 3.0 years ago by
Jackie • 70
• updated
3.0 years ago by
Alex Reynolds ♦ 30k
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For tophat-fusion for gene fusion detection
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For tophat-fusion for gene fusion detection
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3.6 years ago,
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For tophat-fusion for gene fusion detection
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