User: hxlei613

gravatar for hxlei613
hxlei61360
Reputation:
60
Status:
Trusted
Location:
Bangladesh
Last seen:
1 day, 17 hours ago
Joined:
1 year, 10 months ago
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h*******@gmail.com

Posts by hxlei613

<prev • 39 results • page 1 of 4 • next >
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ensembl transcript id to gene symbol using biomart
... Hi. I am using biomart to convert ensembl transcript id to gene symbol. However there seems to be something wrong. Because in the output there is an ensembl transcript id which has two symbol. Here are my script. > ensembl <- useMart(host="dec2013.archive.ensembl.org", biomart = "ENSEMBL_ ...
R biomart ensembl written 5 days ago by hxlei61360 • updated 4 days ago by Emily_Ensembl12k
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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 3 months ago by hxlei61360 • updated 3 months ago by Devon Ryan70k
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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 3 months ago by hxlei61360 • updated 3 months ago by devenvyas390
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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 4 months ago by hxlei61360 • updated 4 months 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 4 months 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 5 months 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 5 months 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 6 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 10 months ago by hxlei61360 • updated 9 months ago by Santosh Anand2.8k
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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 11 months ago by hxlei61360

Latest awards to hxlei613

Student 4 months ago, asked a question with at least 3 up-votes. For Question about MEDIPS
Popular Question 5 months ago, created a question with more than 1,000 views. For Questions about DAVID
Supporter 11 months ago, voted at least 25 times.

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