bissnp-help

Due to the services permanently shut down at USC Epigenome Center, the Bis-SNP website has been

Hi Ermelin, It is better for you to use higher memory, the default is 10G. We have some internal bam

In Bisulfite-seq, the second end read is from the complementary of original +/- strand, But it is

Hi, I have recently downloaded BisSNP and am in the process of having it installed onto my computing

Hi Yaping, Ok, thanks for your answer. Best, Marie-Joe On Wed, Apr 18, 2018 at 10:45 AM, Yaping Liu

Hii... I am getting two different sets of SNP results from same bam file when i used twi different

Hi Marie-Joe, Bis-SNP is designed specifically for the case you described. Are you using

Hi Divya, Sorry for my mistake. 20 should be the parameters, not 30 Yaping Sent from my iPhone On Apr

Hello, Thank you for developing this tool. I am working with soybean varieties and I do not have any

Dear Yaping, I need an output (.bed or .bedgraph) with the following columns: <chromosome> <

Yes, this is the case. Thank you very much, Yaping. Barbara On 1 February 2016 at 19:50, ping <

Hi, I have RRBS data for 20 individuals (n=10 per treatment). I am wondering if I should run BisSNP

Hi, How to calculate SB (Strand Bias) in Bis-SNP? I found the SB value produced in snp.raw.vcf is

Hi, Would it possible to have utilities files for mm10 similar to you made available for other

Dears, This is just an email to report some performance metrics from BisSNP runs we are doing. We

Dears, I am testing BisSNP on a range of WGBS files, average 30x but some of them up to 120x. I want

Just to add to this, the occurrence in chr3 is reproducible in my BAM in the rheMac3 genome at

I am working with RRBS data using hg38 genome reference. For SNP and methylation calling I was

Hi Yaping, I found the bissnp_easy_usage.pl calls MarkDuplicates.jar in picard. But the latest picard

I think it may have to do with my BAM alignment files. Recently I tried BisSNP on BSMAP-aligned files

thanks a lot for your quick reply! On Monday, June 15, 2015 at 11:09:21 AM UTC-4, yaping liu wrote:

Hi All, I am looking for new version of BisSNP. I used at the moment 0.82.2. Kind Regards Kapil

Hi Yaping, yes, I have tested on single sample, it is still running very, very slowly, so slow as to

If you work in the terminal you should be able to run it in java On Tuesday, April 21, 2015 at 2:01:

Hi Anna, Vcf2bed.pl is used to transform methylation vcf to bed format. When CG position is

Hi my question is about SNP calling and I guess is more general than in the context of Bis-SNP. When

Thank you, that worked perfectly. I was able to execute all the example code in the manual. -Jana On

Hi Raphael, Sorry for the late reply! The option for non-directional is "-nonDirectional"

DP4 are not used for genotyping in WGBS, just to match the VCF v4.1 format requirement. BCR6 are more

Hi Annie, You could try this option to adjust mapping quality threshold,-mmq 20 and this option could

Hi Yaping, Thanks very much for the advice! -John On Thursday, September 4, 2014 6:43:20 PM UTC-4,

I want to genotype some bisulfite converted DNA. At this point I already have the methylation data so

Hi Sung, Sorry about the service down. It is up now~~ yaping On Mon, Aug 18, 2014 at 12:35 PM,