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BISulfite-seq CUI Toolkit
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bam generated with bwa-meth #17

Open PoisonAlien opened 7 years ago

PoisonAlien commented 7 years ago

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 ?

wangyunpengbio commented 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
shenhui1986 commented 7 years ago

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.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/zwdzwd/biscuit/issues/17#issuecomment-320414327, or mute the thread https://github.com/notifications/unsubscribe-auth/ABTEUcNl2zcNZ-yr3bVRdnicgjQGwHTKks5sVADTgaJpZM4MN37P.

wangyunpengbio commented 7 years ago

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.

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