BS-Snper
BS-Snper copied to clipboard
hellbelly
Hi, I have run BS-SNPer on my bismark alignments and it seems to have run properly (I get SNP output files), however, in the error file I get several errors...
Is there a way to call SNP variants across multiple files simultaneously with BS-SNPer? It works fine with bam files containing data from a single sample but it does not...
作者，你好，非常高兴能用上这么优秀的软件，不过我目前对你在文献中列出的12种突变情况的原理还是有点疑惑？  对于T>C和C>T的突变中，为什么是打叉？而不是蓝色的点呢？不是能通过Cr 链来获取得到突变信息吗？我理解的3个符号的意思是： - ✔：表明只用当前链即可判断突变情况； - 蓝色点表明单用当前链不能判断突变情况，需要用到对应的Cr链； - 打红色叉表示当前链和Cr链均不能判断是否突变； 我不知道我的理解对不对，还烦请明白的大佬指教！
Hi team, I tried BS-Snper on my RRBS data. The methylation calling and intermediate files were generated, but the final output is empty, however. I followed exactly your example code,...
Hi, Can I use BS-SNPer on bissmark aligned bam files? Thank you.
Hey, in .vcf there are many tags like this: chr1 924310 . C G 49 PASS **DP=5**;ADF=0,5;ADR=0,12;**AD=0,17**; GT:**DP**:ADF:ADR:**AD**:BSD:BSQ:ALFR 1/1:**5**:0,5:0,12:**0,17**:0,0,0,5,12,0,0,0:0,0,0,39,39,0,0,0:0.000,3.400 chr1 924321 . C G 58 PASS **DP=8**;ADF=0,8;ADR=0,13;**AD=0,21**; GT:**DP**:ADF:ADR:**AD**:BSD:BSQ:ALFR 1/1:**8**:0,8:0,13:**0,21**:0,0,0,8,13,0,0,0:0,0,0,38,39,0,0,0:0.000,2.625 chr10...
Hello, I'm trying to learn how to use BS-SNPer for a project I'm working on that used BisSNP. Unfortunately, since BisSNP is not working for me, I am trying to...
Is there a way to get this to output ref/ref (0/0) genotypes? I want to be able to compare different samples and need the allele counts regardless of genotype.
I am receiving the following error. The issue appears to be that samtools isn't in my BS-Snper directory. It is installed on its own. Can't exec "/shared/bin/BS-Snper/samtools-0.1.19/samtools": Permission denied at...