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Dean Thompson
7/25/19
Usage Questions
Hi, I have recently downloaded BisSNP and am in the process of having it installed onto my computing
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Usage Questions
Hi, I have recently downloaded BisSNP and am in the process of having it installed onto my computing
7/25/19
Marie-Joe Karam
,
Yaping Liu
3
4/18/18
Q&A
dbSNP in Bissnp
Hi Yaping, Ok, thanks for your answer. Best, Marie-Joe On Wed, Apr 18, 2018 at 10:45 AM, Yaping Liu
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Q&A
dbSNP in Bissnp
Hi Yaping, Ok, thanks for your answer. Best, Marie-Joe On Wed, Apr 18, 2018 at 10:45 AM, Yaping Liu
4/18/18
Alim Junaid
3/31/18
getting two different sets of results from same bam file
Hii... I am getting two different sets of SNP results from same bam file when i used twi different
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getting two different sets of results from same bam file
Hii... I am getting two different sets of SNP results from same bam file when i used twi different
3/31/18
Marie-Joe Karam
,
Yaping Liu
2
3/16/18
Methyl calling on C polymorphism present in the reads but not in the reference genome
Hi Marie-Joe, Bis-SNP is designed specifically for the case you described. Are you using
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Methyl calling on C polymorphism present in the reads but not in the reference genome
Hi Marie-Joe, Bis-SNP is designed specifically for the case you described. Are you using
3/16/18
Divya Srivastava
,
Lyping1986
4
4/5/17
Q&A
BisSNP generate empty output file
Hi Divya, Sorry for my mistake. 20 should be the parameters, not 30 Yaping Sent from my iPhone On Apr
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Q&A
BisSNP generate empty output file
Hi Divya, Sorry for my mistake. 20 should be the parameters, not 30 Yaping Sent from my iPhone On Apr
4/5/17
Aditi Rambani
3/9/17
Recalibration without known SNPs
Hello, Thank you for developing this tool. I am working with soybean varieties and I do not have any
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Recalibration without known SNPs
Hello, Thank you for developing this tool. I am working with soybean varieties and I do not have any
3/9/17
Barbara Zambiasi Martinelli
8/26/16
methylation count
Dear Yaping, I need an output (.bed or .bedgraph) with the following columns: <chromosome> <
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methylation count
Dear Yaping, I need an output (.bed or .bedgraph) with the following columns: <chromosome> <
8/26/16
Yaping Liu
, …
Barbara Zambiasi Martinelli
9
2/1/16
Re: BisSNP
Yes, this is the case. Thank you very much, Yaping. Barbara On 1 February 2016 at 19:50, ping <
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Re: BisSNP
Yes, this is the case. Thank you very much, Yaping. Barbara On 1 February 2016 at 19:50, ping <
2/1/16
Mackenzie Gavery
11/19/15
should the input .bam be merged?
Hi, I have RRBS data for 20 individuals (n=10 per treatment). I am wondering if I should run BisSNP
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should the input .bam be merged?
Hi, I have RRBS data for 20 individuals (n=10 per treatment). I am wondering if I should run BisSNP
11/19/15
zhaoz...@gmail.com
11/19/15
How to calculate SB (Strand Bias) in Bis-SNP
Hi, How to calculate SB (Strand Bias) in Bis-SNP? I found the SB value produced in snp.raw.vcf is
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How to calculate SB (Strand Bias) in Bis-SNP
Hi, How to calculate SB (Strand Bias) in Bis-SNP? I found the SB value produced in snp.raw.vcf is
11/19/15
kamal.fa...@gmail.com
11/18/15
utilities files
Hi, Would it possible to have utilities files for mm10 similar to you made available for other
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utilities files
Hi, Would it possible to have utilities files for mm10 similar to you made available for other
11/18/15
Albert Vilella
11/13/15
bissnp speed stats
Dears, This is just an email to report some performance metrics from BisSNP runs we are doing. We
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bissnp speed stats
Dears, This is just an email to report some performance metrics from BisSNP runs we are doing. We
11/13/15
Albert Vilella
11/1/15
gvcf output in BisSNP?
Dears, I am testing BisSNP on a range of WGBS files, average 30x but some of them up to 120x. I want
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gvcf output in BisSNP?
Dears, I am testing BisSNP on a range of WGBS files, average 30x but some of them up to 120x. I want
11/1/15
Will Liao
2
10/15/15
Q&A
Illegal "N" character causing error?
Just to add to this, the occurrence in chr3 is reproducible in my BAM in the rheMac3 genome at
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Q&A
Illegal "N" character causing error?
Just to add to this, the occurrence in chr3 is reproducible in my BAM in the rheMac3 genome at
10/15/15
Esita Chattopadhyay
8/29/15
Q&A
Is hg38 indel file available?
I am working with RRBS data using hg38 genome reference. For SNP and methylation calling I was
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Q&A
Is hg38 indel file available?
I am working with RRBS data using hg38 genome reference. For SNP and methylation calling I was
8/29/15
Ke Hu
8/19/15
outdated bissnp_easy_usage.pl
Hi Yaping, I found the bissnp_easy_usage.pl calls MarkDuplicates.jar in picard. But the latest picard
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outdated bissnp_easy_usage.pl
Hi Yaping, I found the bissnp_easy_usage.pl calls MarkDuplicates.jar in picard. But the latest picard
8/19/15
RS
,
ping
4
7/20/15
Q&A
Many more A -> G and T -> C mutations than expected
I think it may have to do with my BAM alignment files. Recently I tried BisSNP on BSMAP-aligned files
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Q&A
Many more A -> G and T -> C mutations than expected
I think it may have to do with my BAM alignment files. Recently I tried BisSNP on BSMAP-aligned files
7/20/15
Lorena Pantano
,
ping
3
6/15/15
in DEFAULT FOR TCGA, are all SNP called without CpG context called as well?
thanks a lot for your quick reply! On Monday, June 15, 2015 at 11:09:21 AM UTC-4, yaping liu wrote:
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in DEFAULT FOR TCGA, are all SNP called without CpG context called as well?
thanks a lot for your quick reply! On Monday, June 15, 2015 at 11:09:21 AM UTC-4, yaping liu wrote:
6/15/15
bissnp-help
6/8/15
Bis-SNP new website!!
Due to the services permanently shut down at USC Epigenome Center, the Bis-SNP website has been
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Bis-SNP new website!!
Due to the services permanently shut down at USC Epigenome Center, the Bis-SNP website has been
6/8/15
kapil jhalani
5/19/15
New Version of Bissnp
Hi All, I am looking for new version of BisSNP. I used at the moment 0.82.2. Kind Regards Kapil
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New Version of Bissnp
Hi All, I am looking for new version of BisSNP. I used at the moment 0.82.2. Kind Regards Kapil
5/19/15
bruce moran
,
ping
3
5/6/15
Extremely Slow BisulfiteGenotyper
Hi Yaping, yes, I have tested on single sample, it is still running very, very slowly, so slow as to
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Extremely Slow BisulfiteGenotyper
Hi Yaping, yes, I have tested on single sample, it is still running very, very slowly, so slow as to
5/6/15
Gema Sanz
,
Tauras V
2
4/21/15
Run bisSNP.jar file under Windows
If you work in the terminal you should be able to run it in java On Tuesday, April 21, 2015 at 2:01:
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Run bisSNP.jar file under Windows
If you work in the terminal you should be able to run it in java On Tuesday, April 21, 2015 at 2:01:
4/21/15
sco...@gmail.com
,
ping
2
3/25/15
vcf2bed
Hi Anna, Vcf2bed.pl is used to transform methylation vcf to bed format. When CG position is
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vcf2bed
Hi Anna, Vcf2bed.pl is used to transform methylation vcf to bed format. When CG position is
3/25/15
Raphaël Poujol
3/2/15
SNP calling
Hi my question is about SNP calling and I guess is more general than in the context of Bis-SNP. When
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SNP calling
Hi my question is about SNP calling and I guess is more general than in the context of Bis-SNP. When
3/2/15
jana.a...@gmail.com
,
ping
5
2/24/15
Problem when running the example
Thank you, that worked perfectly. I was able to execute all the example code in the manual. -Jana On
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Problem when running the example
Thank you, that worked perfectly. I was able to execute all the example code in the manual. -Jana On
2/24/15
Zhiyuan Chen
, …
ping
7
2/24/15
Q&A
Knon SNPs, non-directional, paired vs. single end reads,
Hi Raphael, Sorry for the late reply! The option for non-directional is "-nonDirectional"
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Q&A
Knon SNPs, non-directional, paired vs. single end reads,
Hi Raphael, Sorry for the late reply! The option for non-directional is "-nonDirectional"
2/24/15
annie...@gmail.com
,
ping
2
11/5/14
Q&A
do DP4 values represent converted or unconverted values?
DP4 are not used for genotyping in WGBS, just to match the VCF v4.1 format requirement. BCR6 are more
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Q&A
do DP4 values represent converted or unconverted values?
DP4 are not used for genotyping in WGBS, just to match the VCF v4.1 format requirement. BCR6 are more
11/5/14
annie...@gmail.com
,
ping
4
9/25/14
Q&A
large discrepancy between DP and DP4 in vcf file
Hi Annie, You could try this option to adjust mapping quality threshold,-mmq 20 and this option could
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Q&A
large discrepancy between DP and DP4 in vcf file
Hi Annie, You could try this option to adjust mapping quality threshold,-mmq 20 and this option could
9/25/14
John Lin
,
ping
3
9/4/14
Split by chromosome - downstream effects?
Hi Yaping, Thanks very much for the advice! -John On Thursday, September 4, 2014 6:43:20 PM UTC-4,
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Split by chromosome - downstream effects?
Hi Yaping, Thanks very much for the advice! -John On Thursday, September 4, 2014 6:43:20 PM UTC-4,
9/4/14
annie...@gmail.com
9/2/14
understanding genotyping output modes
I want to genotype some bisulfite converted DNA. At this point I already have the methylation data so
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understanding genotyping output modes
I want to genotype some bisulfite converted DNA. At this point I already have the methylation data so
9/2/14