User: field654
field654 • 10
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- Location:
- China/HangZhou/TigerTCR
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 5 months, 3 weeks ago
- Email:
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Cancer Immunology
Adoptive T cell therapies
Posts by field654
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... I had the same confusion. Why add .86? How is it different? ...
written 8 weeks ago by
field654 • 10
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... Hi Genomax,
The QualiMap worked for me fine. Thanks a lot.
I have an additional question. Regarding the QC reports, I have duplicatioin rates from both my samples (WES, 13GB data each) of around 50%.
I wonder if that's to be expected or too high.
Best,
Field
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written 3 months ago by
field654 • 10
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... Thank you so much for getting back to me, Genomax. I will try out. ...
written 3 months ago by
field654 • 10
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... I used to use Bowtie2 and it gives the results
"Out of xxxxxxxxx reads, yyyyyyyy have been aligned 0 times, zzzzzz have been aligned exactly once....."
I just tried out the BWA but didn't see the counterpart. I wonder if there's any so I can compare.
Many thanks.
Field ...
written 3 months ago by
field654 • 10
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Comment:
C: GATK Mutect2 tumor mode
... HI Cocchi,
Although I haven't gone through deeply, I believe you should check out this link where the GATK group described the usage of Mutect2 for a paired t-n tissues. It's updated 14 days ago. Not sure if it serves your WGS data though.
[https://gatk.broadinstitute.org/hc/en-us/articles/3600358 ...
written 3 months ago by
field654 • 10
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... Hi Colin,
Thank you for providing the resource. Although I had some glitch when registering for the TCRB account, I have fianlly got access to the data. That's exactly what I've been searching for. ...
written 4 months ago by
field654 • 10
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... Hi Colin,
Thank you so much for the resource. I don't even know there's a journal just about data. I would try out asap and mark the question as anwsered.
Best,
Field
...
written 4 months ago by
field654 • 10
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... Sorry I forgot to thank you for the GATK recommended pipeline. As a beginner bioinformatic practitioner, I basically struggle between a few available programs for each step of data analyzing. Papers do compare them but rarely give an absolute pick. I would definiely go-over the gatk pipeline and see ...
written 4 months ago by
field654 • 10
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... Hi ATpoint,
Thank you so much for the reply. I've been working on a pair of breast cancer tissues.
Unfortunately I can't put in a whole lot of time into literature searching. I did limited searching but found none providing raw data. Maybe the raw data is too large for download. Also, I emailed t ...
written 4 months ago by
field654 • 10
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... I've been trying to analyze a pair of tumor/margin tissues but got very few meaningful somatic mutations.
I doubt if I picked the correct pipeline/parameters.
I wonder if there's any publications made with similar samples where the authors provided the raw data that I can download and run with my ...
written 4 months ago by
field654 • 10
• updated
4 months ago by
colindaven • 2.6k
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