User: Jackie
Jackie • 60
- Reputation:
- 60
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 6 years, 2 months ago
- Email:
- d*******@gmail.com
about me
Posts by Jackie
<prev
• 38 results •
page 1 of 4 •
next >
0
votes
1
answer
214
views
1
answers
... Sorry about the confusion, and thanks for providing the hyperlink.
I have updated the post by inserting the hyperlink for Mitelman. ...
written 4 months ago by
Jackie • 60
0
votes
1
answer
214
views
1
answers
... 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 4 months ago by
Jackie • 60
0
votes
1
answer
214
views
1
answer
... 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 ...
0
votes
0
answers
242
views
0
answers
... 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 5 months ago by
Jackie • 60
0
votes
0
answers
242
views
0
answers
... Can anyone please help with this question?
Thanks a lot! ...
written 5 months ago by
Jackie • 60
0
votes
0
answers
242
views
0
answers
... 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 5 months ago by
Jackie • 60
0
votes
0
answers
365
views
0
answers
... 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 11 months ago by
Jackie • 60
0
votes
2
answers
837
views
2
answers
... 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 12 months ago by
Jackie • 60
0
votes
2
answers
837
views
2
answers
... 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 12 months ago by
Jackie • 60
4
votes
2
answers
837
views
5 follow
2
answers
... 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 12 months ago by
Jackie • 60
• updated
12 months ago by
Alex Reynolds ♦ 25k
Latest awards to Jackie
Popular Question
11 months ago,
created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
Popular Question
15 months ago,
created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
Popular Question
19 months ago,
created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 633 users visited in the last hour