Open PoisonAlien opened 7 years ago
It seems that I have encountered the sam problem.My script is:
biscuit pileup -r index/hg19.fa -i sams/SRR1282202.align.sort.bam -o SRR1282202.vcf -q 20
bgzip SRR1282202.vcf
tabix -p vcf SRR1282202.vcf.gz
biscuit vcf2bed -t hcg SRR1282202.vcf.gz > SRR1282202.hcg.bed &
biscuit vcf2bed -t gch SRR1282202.vcf.gz > SRR1282202.gch.bed &
And the result file(SRR1282202.hcg.bed and SRR1282202.gch.bed)contains nothing.### What's wrong with it? However,using -t cg -t snp -t c ,I have got some results.
biscuit vcf2bed -k 10 -t cg SRR1282202.vcf.gz > SRR1282202.cg.bed
biscuit vcf2bed -k 10 -t snp SRR1282202.vcf.gz
biscuit vcf2bed -t c SRR1282202.vcf.gz > SRR1282202.c.bed
Hi just letting everyone know that Wanding is currently away on vacation and won’t return until two weeks later. I doubt that he will receive these emails in China as gmail is blocked. I will give this a test next week and see what I find and report back to you. It’s a hectic week for me so perhaps will take a few days before I’ll be able to sit down and work on it. Thanks all!
Thanks, Hui
Hui Shen, Ph.D. Assistant Professor, Van Andel Research Institute Center for Epigenetics Room 5004W 333 Bostwick Ave., N.E. Grand Rapids, Michigan 49503-2518 U S A
Phone: 616-234-5362 Fax: 616-234-5562 email: hui.shen@vai.org https://shenlab.vai.org
On Aug 5, 2017, at 1:42 AM, wangyunpengbio notifications@github.com wrote:
It seems that I have encountered the sam problem.
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Thanks for your prompt action.Actually,when I use biscuit to generate bam file.I still the same result and don't get the HCG and GCH result.
biscuit align -t 12 index/hg19.fa fastq/SRR1282202_1.fastq.gz fastq/SRR1282202_2.fastq.gz | samtools sort -T . -O bam -o bams/SRR1282202.bam
samtools index bams/SRR1282202.bam
biscuit tview -g chr19:7525080 SRR1282202.bam index/hg19.fa
biscuit pileup -r index/hg19.fa -i SRR1282202.bam -o SRR1282202.vcf -q 20
bgzip SRR1282202.vcf
tabix -p vcf SRR1282202.vcf.gz
biscuit vcf2bed -k 10 -t cg SRR1282202.vcf.gz > SRR1282202.cg.bed &
biscuit vcf2bed -k 10 -t snp SRR1282202.vcf.gz > SRR1282202.snp.bed &
biscuit vcf2bed -t c SRR1282202.vcf.gz > SRR1282202.c.bed &
biscuit vcf2bed -t hcg SRR1282202.vcf.gz > SRR1282202.hcg.bed &
biscuit vcf2bed -t gch SRR1282202.vcf.gz > SRR1282202.gch.bed &
SRR1282202.c.bed ,SRR1282202.cg.bed and SRR1282202.snp.bed have result. But SRR1282202.hcg.bed and SRR1282202.gch.bed are nothing in them.
System Information Distributor ID: Ubuntu Description: Ubuntu 16.04.2 LTS Release: 16.04 Codename: xenial
I aligned my Nome-seq reads with bwa-meth. Now I want to look at ndr and endogenous methylation. Following your protocol, I need to generate vcf. Does the bam file and index generated by bwa-meth compatible with biscuit ?