User: Tommy Au

gravatar for Tommy Au
Tommy Au70
Reputation:
70
Status:
New User
Location:
Hong Kong
Website:
http://tommyau.hk/
Scholar ID:
Google Scholar Page
Last seen:
4 months ago
Joined:
2 years, 6 months ago
Email:
c*********@gmail.com

Posts by Tommy Au

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Amplicon sequencing: how to handle adapters and primers?
... If your amplicon panel does not have any overlapping amplicons, removing primer or not depends on whether you expect and tolerate missing "rare cases", e.g. SNV or INDEL near gene-specific primers. It depends on the genes of interest and the panel design in the context of variant types and location. ...
written 9 months ago by Tommy Au70
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... Thank you for your comments. We described the case in details at [Scientific Reports 7:1567][1]. [1]: https://www.nature.com/articles/s41598-017-01703-6 ...
written 14 months ago by Tommy Au70
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... We exactly did such FASTQ hard trimming for variant calling purpose but almost missed a germline BRCA1 17-nt deletion in a hereditary breast cancer patient. ...
written 14 months ago by Tommy Au70
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Comment: C: primer trimming tools
... We also adopted the workflow of BWA-MEM alignment first and then soft-clip primer afterwards. Since ours are nested amplicons, GATK ClipReads cannot properly handle the primer clipping. We then developed and use [BAMClipper][1] ([Scientific Reports 7:1567][2]). The bonus is that errors in primer seq ...
written 14 months ago by Tommy Au70
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... For nested amplicon sequencing, we first align the original reads (having primer sequences) to reference and then mask the primers by soft-clipping the alignments using [BAMClipper][1] ([Scientific Reports 7:1567][2]). As mentioned in [another thread][3], primer trimming at FASTQ level (1) is comput ...
written 14 months ago by Tommy Au70
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Answer: A: Limiting variant calls to amplicon target regions?
... Primer trimming at FASTQ level (1) is computationally expensive, (2) incorrectly handles nested PCR amplicons, (3) makes indels harder to detect by conventional variant calling. [BAMClipper][1] is demonstrated to remove PCR primers by soft-clipping BAM alignments ([Scientific Reports 7:1567][2]), so ...
written 14 months ago by Tommy Au70
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Answer: A: Removing PCR primers in targeted sequencing with nested amplicons
... [BAMClipper][1] is designed to remove PCR primers in nested amplicon NGS setting ([Scientific Reports 7:1567][2]). [1]: https://github.com/tommyau/bamclipper [2]: https://www.nature.com/articles/s41598-017-01703-6 ...
written 14 months ago by Tommy Au70
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Answer: A: How to do INDEL alignment
... If your goal to have such "ideal alignment" is accurately calling the variant as a single variant in VCF format (complex indel), you may want to take a look at [INDELseek](https://github.com/tommyau/indelseek), which calls such complex indel directly from the BWA alignments. I tried to reproduce yo ...
written 19 months ago by Tommy Au70 • updated 19 months ago by Chris Miller20k
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Answer: A: Identifying FLT3-ITD with Pindel
... ITDseek is designed to detect FLT3 ITD in amplicon NGS reads https://github.com/tommyau/ITDseek ...
written 2.5 years ago by Tommy Au70

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