User: hxlei613

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hxlei61360
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Location:
Bangladesh
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14 hours ago
Joined:
1 year, 7 months ago
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Posts by hxlei613

<prev • 38 results • page 1 of 4 • next >
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Question about details of the calculation of bisulfite conversion rates.
... Hi! I wonder some details about the calculation of bisulfite conversion rates. 1. It seems that conversion rate can be calculated using all types of C ( CpG, CHH, CHG ) ? 2. How about the coverage of every single C? 5X or 10x ? Is there a threshold ? Another question about CpG methylation rates: ...
bisulfite conversion rates written 5 days ago by hxlei61360 • updated 4 days ago by Devon Ryan65k
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How to call mitochondrial SNP?
... Hello. I have searched this question on biostars already.But I am not satisfied with the result. MitoSeek need a control to call mutation.Well I dont have a control. I have seen many papers said they used GATK but they didnt clearify UnifiedGenotyper or HaplotypeCaller. I also see someone try to use ...
mitochondrial snp written 28 days ago by hxlei61360 • updated 28 days ago by devenvyas340
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(Closed) Heteroplasmy and homoplasmy in mtDNA
... I have read some papers inorder to get a better understanding about heteroplasmy and homoplasmy in mtDNA. But I am still confused about the definition of heteroplasmy and homoplasmy . Could someone please give an easily undertanding explaination ? Thank you very much! ...
mtdna heteroplasmy homoplasmy written 5 weeks ago by hxlei61360 • updated 5 weeks ago by jotan1.1k
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Comment: C: Bias plot from targeted bisulfite sequencing
... Hi,I wonder how to draw a mbias plot using bwameth ? I cant find the script on github.Thank you very much! ...
written 6 weeks ago by hxlei61360
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Comment: C: CpG coverage of BS-seq ?
... Hi, I updated my question to make sure I have expressed myself clearly. Thank you very much! ...
written 11 weeks ago by hxlei61360
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CpG coverage of BS-seq ?
... Hello,I have a question about the CpG coverage of BS-seq. In general many papers would say that how many CpGs are covered by their RRBS experiments. I wonder what is the definition of the CpG. Here is an example: + 5' ---CG---3' - 3' ---GC---5' My question is : Are there two CpGs or just one C ...
bs-seq written 11 weeks ago by hxlei61360
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DMAP for RRBS generate blank output
... Hello everyone! Lately I've been using DMAP to analyse my RRBS. Trimming(trim_galore), mapping(bismark) all seem fine. DMAP works well with test data supplied by [DMAP][1]. However when I use my raw bam generated by bismark, DMAP doesn't generate any output and there is no error message.I don't know ...
rrbs dmap written 3 months ago by hxlei61360
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Possible bug for bismark when methylation calling ?
... Hi, I'm using bismark for bs-seq mapping and methylation calling. I take a glance at the coverage file generated by *bismark2bedGraph*. However, the result seems strange. Take CpG site of chrM for example (because chrM is the smallest chromosome). The coverage file contains sites that are not CpG si ...
methylation bs-seq bismark written 7 months ago by hxlei61360 • updated 6 months ago by Santosh Anand2.2k
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Comment: C: Filter a sam file by alignment score.
... AS tag, it means alignment score.I am using bwa( bwa aln and bwa sampe ). ...
written 8 months ago by hxlei61360
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Comment: C: Filter a sam file by alignment score.
... I just want to filter reads with alignment scores less than 1 before subsequent analysis. ...
written 8 months ago by hxlei61360

Latest awards to hxlei613

Student 6 weeks ago, asked a question with at least 3 up-votes. For Question about MEDIPS
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Questions about DAVID
Supporter 8 months ago, voted at least 25 times.

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