User: MatthewP

gravatar for MatthewP
MatthewP10
Reputation:
10
Status:
New User
Location:
China
Last seen:
1 week ago
Joined:
2 months, 3 weeks ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 17 results • page 1 of 2 • next >
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Comment: C: How to download dataset from MITOMAP?
... Thanks, that's exactly what I want. ...
written 28 days ago by MatthewP10
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Hello, this is not a valid VCF format, check [here][1] for the right VCF format. [1]: https://samtools.github.io/hts-specs/VCFv4.2.pdf ...
written 29 days ago by MatthewP10
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Comment: C: Removing Duplicates before aligning
... Wow, thanks for your answer. I also have some amplicon-based data and I didn't do mark duplicates job because [fastp][1] shows the duplication rates is more than 96%. Now I know I should use vsearch to mark duplicates. [1]: https://www.biorxiv.org/content/early/2018/03/01/274100 ...
written 4 weeks ago by MatthewP10
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Comment: C: How to download dataset from MITOMAP?
... Ok, that's what I am doing, thanks for you reply! ...
written 5 weeks ago by MatthewP10
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How to download dataset from MITOMAP?
... Hello all! I want to **download dataset** offered by [MITOMAP][1]. Here's what I want to download: mtDNA Variants (includes mini insertions & deletions) - [Control Region Variants (16024-576)][2] - [Coding & RNA Variants (577-16023, MTTF-MTTP)][3] mtDNA Mutations with Reports of Disease ...
mtdna database mitomap written 5 weeks ago by MatthewP10
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How to keep sample name while using samtools mpileup + varscan to do variant call?
... Hello, everyone. I am using **samtools mpileup** and **[varscan][1]** to do variant call, but this will lost all the sample names. For example if I have 10 bam file name like `18R07049.bam ... 18R07058.bam`, I pileup them all to `18R07.mpileup`: samtools mpileup -f myref.fasta -o 18R07.mpileup ...
varscan samtools mpileup written 6 weeks ago by MatthewP10 • updated 6 weeks ago by Pierre Lindenbaum111k
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Do I need to mark duplicates for sequencing data using multiplex PCR to prepare library?
... Hello. I have some **mtDNA** sequencing data using multiplex PCR to prepare library, which means using many primers to 'copy' whole mtDNA from whole genome DNA by PCR, then use those fragments to perform sequencing. I used **[fastp][1]** to filtered my raw data, and the result shows: Filtering ...
mtdna picard multiplex pcr written 6 weeks ago by MatthewP10 • updated 6 weeks ago by finswimmer4.4k
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Comment: C: Some questions about write human mitochondrial variants into VCF file
... We like to set our own pipelines so it's easy to maintains and upgrade. Thank you very much I will try your pipeline. ...
written 7 weeks ago by MatthewP10
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Comment: C: Some questions about write human mitochondrial variants into VCF file
... Well, I work in a company offering sequencing service. This is our company first time received mtDNA order. Our client want us to analyse heterogeneous of mtDNA(variants) and copy number variants(CNV). They are using multi-PCR to obtain mtDNA library, so I think we can't get CNV from such data, the ...
written 7 weeks ago by MatthewP10
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Comment: C: Some questions about write human mitochondrial variants into VCF file
... Thank you! Can I have your e-mail address? I will send e-mail to discuss with you. ...
written 7 weeks ago by MatthewP10

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