User: bill-zt

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bill-zt40
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Posts by bill-zt

<prev • 10 results • page 1 of 1 • next >
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Pairwisely detecting primer secondary structure: too many groups
... I designed a NGS PANEL for human lung cancer related genes using multiplex PCR strategy. This PANEL contains ~6000 PCR primers that have highly specificity across the whole human genome. Now I need to do the last step: Pairwisely detecting secondary structures between any of the two primers and then ...
pairwise secondary structure primer themodynamic written 6 weeks ago by bill-zt40
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Oncotype DX 21-gene panel: How to do qRT-PCR normalization?
... Oncotype DX 21-gene panel is a popular panel for breast-cancer recurrent prediction and has been cited ~thousands times (See DOI: 10.1056/NEJMoa041588 ). What confused me a lot is the first step of expression level normalization for 16 cancer-related genes. Almost every literature wrote: For each s ...
normalization qrt-pcr breast cancer oncotype dx written 12 weeks ago by bill-zt40
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Tool: PrimerServer: a high-throughput primer design and specificity-checking platform
... We are happy to release **PrimerServer**, a high-throughput primer design and specificity-checking platform. ## Project Page ## https://github.com/billzt/PrimerServer ## Demo Server ## https://primerserver.org ## Pre-Print ## Zhu T, Liang CZ, Meng ZG, Li YY, Wu YY, Guo SD* and Zhang R* (2017). P ...
primer tool blast pcr written 9 months ago by bill-zt40
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Comment: C: fastest method to get potential amplicons based on paired-primers
... However primerblast is only available as a web interface, no standalone program ...
written 12 months ago by bill-zt40
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Are parent features lines always appear before sub-feature lines in GFF3 files?
... In GFF3 file, there are parent features lines and sub-feature lines like: I SGD gene 335 649 . + . ID=gene:YAL069W;biotype=protein_coding; I SGD mRNA 335 649 . + . ID=transcript:YAL069W;Parent=gene:YAL069W;biotype=protein_coding Usually, parent features lines (such as gene) **should appe ...
gff3 genome annotation written 12 months ago by bill-zt40 • updated 12 months ago by Michael Dondrup44k
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Comment: C: How heterozygous GTs were defined in SNP calling vcf result
... Well, I've used the traditional `bcftools call -c` model. When I switched to `bcftools call -m`, the `GT:PL:DP:SP:AD 0/1:0,0,0:0:0:0,0` has been disappeared ...
written 19 months ago by bill-zt40
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How heterozygous GTs were defined in SNP calling vcf result
... I use samtools-bcftools pipeline to call variations among a sample (30 individuals) with low coverage (~5X each). samtools mpileup -ugf genome.fa -b bam.list -t AD,INFO/AD,DP,SP | bcftools call -vcO z -o out.vcf.gz In the result, I found some strange heterozygous GTs: (1) some heterozygous ...
vcf wgs bcftools samtools snp written 19 months ago by bill-zt40 • updated 19 months ago by Gabriel R.2.4k
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How The Non-Canonical Intron Splice Sites Came Out?
... The canonical intron splicing sites should be GT-AG, GC-AG and AT-AC, while other non-canonical splicing sites are mostly annotation errors. However I still find some non-canonical splicing cases that have good transcriptome support. For example, the fourth intron in ENSMUST00000003725 in mouse (C ...
intron written 4.5 years ago by bill-zt40 • updated 18 months ago by Biostar ♦♦ 20
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Comment: C: How Pindel Find Out Long Inserted Sequence?
... Thank you. And the -z option can report the exact inserted sequence, really? The user manual of pindel does not mention it. ...
written 4.5 years ago by bill-zt40
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How Pindel Find Out Long Inserted Sequence?
... the current version of pindel, v0.2.4, is able to find out and report long insertions. However its user manual didn't note about this. I want to know how it find it, because according to the split reads strategy, it seems impossible. And according to http://seqanswers.com/forums/showthread.php?t=18 ...
pindel written 4.5 years ago by bill-zt40 • updated 4.5 years ago by liangkaiye250

Latest awards to bill-zt

Popular Question 11 months ago, created a question with more than 1,000 views. For How Pindel Find Out Long Inserted Sequence?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For How The Non-Canonical Intron Splice Sites Came Out?

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