User: Haitao

gravatar for Haitao
Haitao20
Reputation:
20
Status:
New User
Location:
Macau University
Website:
http://fhs.umac.mo/
Last seen:
6 months ago
Joined:
11 months, 1 week ago
Email:
x*************@gmail.com

Posts by Haitao

<prev • 15 results • page 1 of 2 • next >
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Comment: C: How to convert bam-readcount output to BED-VAF format
... # From BED-VAF file to extract common paired sample's SNP site info, prepare for sciclone: Extract common SNP site info cat $1.readcounts.bed | tail -n +2 | awk '{print $1"\t"$2"\t"$2}' > $1.bed cat $2.readcounts.bed | tail -n +2 | awk '{print $1"\t"$2"\t"$2}' > $2.bed cat $3.re ...
written 10 months ago by Haitao20
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Answer: A: How to convert bam-readcount output to BED-VAF format
... Dear All, Based on Chris and Monica's advice, Here I have some update for deal with bam-readcount output file. My Colleague and friend help me wrote perl script to convert bam-readcount file to Bed format VAF file. bam-readcount2VAF.pl use strict; use warnings; use LWP::Simple; u ...
written 10 months ago by Haitao20
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Comment: C: How to convert bam-readcount output to BED-VAF format
... Hi Monica, Thanks for sharing this shell command. I test it, It's work well, this is only for SNP not include insert or deletion site. thanks again : ) Haitao ...
written 10 months ago by Haitao20
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Comment: C: How to convert bam-readcount output to BED-VAF format
... Thanks I will try this! ...
written 10 months ago by Haitao20
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Comment: C: How to convert bam-readcount output to BED-VAF format
... Hi Chris, Thanks for your advice, however, I'm not very familiar with perl, I can understand the script but very hard to write script by myself until now, I try to write script by myself but need some time, my level is application level at this moment. I'm work on bench before(~10 years), recent on ...
written 10 months ago by Haitao20
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Comment: C: How to convert bam-readcount output to BED-VAF format
... Wow, you need to sleep now : ), thanks for your answer so fast! Haitao ...
written 10 months ago by Haitao20
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How to convert bam-readcount output to BED-VAF format
... Dear All, When I use bam-readcount to count each SNP position's depth for making %VAF, Especially for those pair samples, only happened mutation in one sample but not in other paired sample, my final goal is for calculate BAF, sciclone input file or %VAF. Here is the code: #Step one: #E ...
loh sciclone snp bam-readcount sequencing written 10 months ago by Haitao20
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Comment: C: sciClone input vaf file?
... Dear Chris, I'm following what you mentioned in this post, I got bam-readcount output file now: GL456392.1 772 C 123 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:103:30.22:36.83:1.46:46:57:0.57:0.06:145.63: ...
written 10 months ago by Haitao20
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Answer: A: sciClone input vaf file?
... Hi Chris, I have one more question for building clonal evolution, since when I use sciclone to calulate subclone, I already remove those un-neutral region, after got subclone info, can I add those CNV changed region back to build evolution event? I ran THetA2 succesfully, I plan use sciclone + THet ...
written 10 months ago by Haitao20
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Comment: C: sciClone input vaf file?
... I will modify my pipeline based on your suggestion. Thanks! Haitao ...
written 10 months ago by Haitao20

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