User: graeme.thorn

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graeme.thorn30
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30
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New User
Location:
London, United Kingdom
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1 day, 22 hours ago
Joined:
3 years, 3 months ago
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g***********@gmail.com

Posts by graeme.thorn

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Variant calling using IonTorrent caller correcting for deamination
... I think, Gabriel R., that I've found the way to deal with this. On inspecting one of my samples (with estimated deamination metric, the proportion of called SNPs consisting of C>T or G>A transitions, of 0.837), this looks like a straightforward filtering procedure. Looking at the minor allele ...
written 9 days ago by graeme.thorn30
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Comment: C: Variant calling using IonTorrent caller correcting for deamination
... That's one possible strategy, though this could throw out lots of important information with regards to the clinical outcomes. The other strategy that I'm playing with is to cluster the called variants on quality and on allele fraction. [C>T] and [G>A] transitions due to the DNA damage are lik ...
written 10 days ago by graeme.thorn30
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Variant calling using IonTorrent caller correcting for deamination
... I'm calling variants using the IonTorrent TorrentSuite on DNA which has been sequenced from formalin-fixed paraffin-embedded tissue. This has a major issue in that without addition of uracil-N-glycosylase, some of the Ts in the original DNA are deaminated to Cs, which upon sequencing and calling var ...
iontorrent variants written 16 days ago by graeme.thorn30
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CNV calling on mapped IonTorrent reads
... I have circa 120 BAM files from IonTorrent Ampli-seq on the ThermoFisher Scientific Comprehensive Cancer Panel. Is the answer given in this question: https://www.biostars.org/p/231354/ still relevant for calling CNV on the mapped results? ...
cnv written 23 days ago by graeme.thorn30
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Filtering IonTorrent variant caller VCFs
... I've got c. 140 VCF files generated by the IonTorrent variant caller pipeline (sequenced using ampliSeq on the comprehensive cancer panel) that I want to process further. However, I'm not sure what filters to apply to the VCFs before grouping them into merged VCFs per group. As far as I can tell, t ...
vcf iontorrent variants written 26 days ago by graeme.thorn30
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Answer: A: IonTorrent variant calling: "Missing ZM: tags"
... It turns out, after speaking to tech support that these are old files from a previous version of the software so won't run through variant caller. The files themselves need reanalysing from the initial FASTQ -> BAM with the newest version. ...
written 4 months ago by graeme.thorn30
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Comment: C: IonTorrent variant calling: "Missing ZM: tags"
... Did do, finally, after fruitless searching - it turns out the files need reanalysing from the start, so raw sequencing to BAM needs redoing before calling variant caller ...
written 4 months ago by graeme.thorn30
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IonTorrent variant calling: "Missing ZM: tags"
... I have a lot of IonTorrent sequencing data in BAM format that I want to call variants on, using the IonTorrent variant caller. However, for some of the BAM files (for about 20 samples out of ~150) the variant caller stops due to what it states are lack of ZM: tags in a few individual reads. The thi ...
ion-torrent variants written 4 months ago by graeme.thorn30
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Comment: C: Downloading triple negative breast cancer data from ICGC
... That data does not contain the receptor status though. The equivalent data for the TCGA data (BRCA-US project) on the GDC does have the receptor status to assess whether its TNBC or not, but the clinical data from the ICGC does not contain it. ...
written 6 months ago by graeme.thorn30
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Comment: C: Downloading triple negative breast cancer data from ICGC
... I can't see any global table like for the GDC, and the clinical data available for each patient does not have the information I need to filter out those who aren't TNBCs ...
written 6 months ago by graeme.thorn30

Latest awards to graeme.thorn

Popular Question 3 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 4 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar 6 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 16 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 3.2 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory

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