User: Yu Chuan Tai

gravatar for Yu Chuan Tai
Yu Chuan Tai440
Reputation:
440
Status:
Trusted
Location:
Last seen:
7 years, 2 months ago
Joined:
13 years, 8 months ago
Email:
y******@stat.berkeley.edu

Posts by Yu Chuan Tai

<prev • 44 results • page 1 of 5 • next >
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... Hi Sean, No worries. I actually want mutant frequencies for each sample, but I didn't see any fucntion in VariantAnnotation for that. Anyway, I just found that samtools/bcftools may calculate that directly. Thanks for your help! Best, Yu Chuan On Sat, 9 Jun 2012, Sean Davis wrote: > On Fri, J ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
672
views
1
answers
Comment: C: Amplicon and exon level read counts and GC content
... Hi Martin, A quick question. Does it matter if I don't have the strand info. for the interval that I am interested in, when I specify the input arguments for ScanBamParam()? Best, Yu Chuan On Thu, 7 Jun 2012, Martin Morgan wrote: > On 06/06/2012 09:53 PM, Yu Chuan Tai wrote: >> Hi Marti ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... Hi Sean, I didn't find any function in the VariantAnnotation package that can calculate mutant freq. Do you mean after reading in a VCF file using readVcf(), I need to calculate the base-level coverage first (for example, using the way Martin had suggested), and convert coverage to frequency mysel ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
672
views
1
answers
Comment: C: Amplicon and exon level read counts and GC content
... Hi Martin, Is it correct that the below code calculate the number of reads overlapping with an amplicon, and overlapping means at least 1 base overlap, and it doesn't have to be fully within the amplicon? In the case that a read overlaps with 2 amplicons, will it be counted twice? When I used this ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... Hi Sean, I see. Thanks for your clarification! Best, Yu Chuan On Thu, 7 Jun 2012, Sean Davis wrote: > On Thu, Jun 7, 2012 at 11:24 AM, Yu Chuan Tai wrote: >> I see. So, which input arguments of scanBamFlag() or ScanBamParam() take >> care of paired-end reads? Or should I even wor ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... Hi Martin, One more question. Is there any way in Rsamtools to calculate SNVs/INDELS frequency directly using the output file from samtools? Thanks! Best, Yu Chuan On Thu, 7 Jun 2012, Martin Morgan wrote: > On 06/06/2012 10:43 PM, Yu Chuan Tai wrote: >> Hi, >> >> Is there an ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... I see. So, which input arguments of scanBamFlag() or ScanBamParam() take care of paired-end reads? Or should I even worry about the paired-end natural when calculating coverage? Thanks! Yu Chuan On Thu, 7 Jun 2012, Sean Davis wrote: > On Thu, Jun 7, 2012 at 11:03 AM, Yu Chuan Tai wrote: >& ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answers
Comment: C: base-specific read counts
... Thanks! In your code below, to take care of the paired-end reads, is it correct that at least I need to set isPaired=TRUE in scanBamFlag()? Best, Yu Chuan On Thu, 7 Jun 2012, Martin Morgan wrote: > On 06/06/2012 10:43 PM, Yu Chuan Tai wrote: >> Hi, >> >> Is there any way to c ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
672
views
1
answers
Comment: C: Amplicon and exon level read counts and GC content
... Hi Martin, Thanks! I will look into the links below. By 'better support for paired-end reads in the 'devel' version', which package are you referring to? Best, Yu Chuan On Thu, 7 Jun 2012, Martin Morgan wrote: > On 06/06/2012 09:53 PM, Yu Chuan Tai wrote: >> Hi Martin, >> >> ...
written 7.2 years ago by Yu Chuan Tai440
0
votes
1
answer
607
views
1
answer
base-specific read counts
... Hi, Is there any way to calculate base-specific read counts for a given genomic interval (including 1-base interval), for paired-end data aligned by Bowtie2 in BAM format? Thanks! Best, Yu Chuan ...
written 7.2 years ago by Yu Chuan Tai440 • updated 7.2 years ago by Martin Morgan ♦♦ 23k

Latest awards to Yu Chuan Tai

Popular Question 7.2 years ago, created a question with more than 1,000 views. For samtools error

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 139 users visited in the last hour