User: bill-zt

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bill-zt40
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Posts by bill-zt

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Bwa Mapping Qualities Of 0
... Hello huskerjeff492, you should notice the following notes: (1) `bwa mem` will ouput the `XA` column **only if** there were `less than 5 hits` by default (can be changed by the -h parameter). It is impossible to list all the alignments if there were thousands hists. (2) according to this sequence ...
written 3 months ago by bill-zt40
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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 7 months ago by bill-zt40 • updated 5 months ago by Biostar ♦♦ 20
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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 8 months 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 15 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 18 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 18 months ago by bill-zt40 • updated 18 months ago by Michael Dondrup45k
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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 2.1 years 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 2.1 years ago by bill-zt40 • updated 2.1 years ago by Gabriel R.2.5k
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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 5.0 years ago by bill-zt40 • updated 24 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 5.0 years ago by bill-zt40

Latest awards to bill-zt

Popular Question 17 months ago, created a question with more than 1,000 views. For How Pindel Find Out Long Inserted Sequence?
Popular Question 4.9 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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