User: field654

gravatar for field654
field65410
Reputation:
10
Status:
New User
Location:
China/HangZhou/TigerTCR
Last seen:
1 month, 3 weeks ago
Joined:
5 months, 3 weeks ago
Email:
f*******@gmail.com

Cancer Immunology

Adoptive T cell therapies

 

Posts by field654

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
3.5k
views
0
answers
Comment: C: Human reference files in HG38 GATK resource bundle
... I had the same confusion. Why add .86? How is it different? ...
written 8 weeks ago by field65410
0
votes
1
answer
160
views
1
answers
Comment: C: Where to check out the alignment results for BWA
... 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 ...
written 3 months ago by field65410
0
votes
1
answer
160
views
1
answers
Comment: C: Where to check out the alignment results for BWA
... Thank you so much for getting back to me, Genomax. I will try out. ...
written 3 months ago by field65410
2
votes
1
answer
160
views
1
answer
Where to check out the alignment results for BWA
... 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 ...
alignment bwa written 3 months ago by field65410
0
votes
0
answers
297
views
0
answers
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 field65410
1
vote
1
answer
194
views
1
answers
Comment: C: Where to find paired solid tumor WES raw data (tumor/tumor margin) that I can do
... 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 field65410
0
votes
1
answer
194
views
1
answers
Comment: C: Where to find paired solid tumor WES raw data (tumor/tumor margin) that I can do
... 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 field65410
0
votes
1
answer
194
views
1
answers
Comment: C: Where to find paired solid tumor WES raw data (tumor/tumor margin) that I can do
... 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 field65410
0
votes
1
answer
194
views
1
answers
Comment: C: Where to find paired solid tumor WES raw data (tumor/tumor margin) that I can do
... 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 field65410
3
votes
1
answer
194
views
1
answer
Where to find paired solid tumor WES raw data (tumor/tumor margin) that I can download?
... 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 ...
snp sequencing written 4 months ago by field65410 • updated 4 months ago by colindaven2.6k

Latest awards to field654

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1095 users visited in the last hour
_