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User: graeme.thorn

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graeme.thorn • 40
Reputation:
40
Status:
New User
Location:
London, United Kingdom
Last seen:
4 days, 18 hours ago
Joined:
3 years, 7 months ago
Email:
g***********@gmail.com

Posts by graeme.thorn

<prev • 30 results • page 1 of 3 • next >
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Varscan settings for ctdna variant calling
... I am analysing some cell-free DNA samples (in the hope of finding variants from circulating tumour DNA) and I am aware of the problems with trying to call variants on such fragmentary DNA data. However, this paper: https://www.nature.com/articles/nature12065 (Murtaza et al, 2013, Non-invasive analy ...
ctdna variants written 24 days ago by graeme.thorn • 40
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Post-filtering WES for mutation calling
... I have some whole exome sequencing data from cell-free DNA (at 500 or 1000X coverage) and have called mutations using the GATK pipeline with Mutect2. However, the results have mutations listed which are not in the exons, alongside all the exon mutations we expect. Examining the original BAM file fr ...
wxs wes mutect2 written 8 weeks ago by graeme.thorn • 40
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Comment: C: Formating RNA-seq with UMIs in unmapped BAM files to UMI-tools compatible FASTQ
... Thanks, just spotted those options --umi-tag and --extract-umi-method=tag. STAR can use unmapped BAM files as input and (according to its docs) retains all tags when mapping so it can be used prior to that. Now just to find a solution to clip/trim the unmapped BAM before trying to align. ...
written 11 weeks ago by graeme.thorn • 40
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Comment: C: Formating RNA-seq with UMIs in unmapped BAM files to UMI-tools compatible FASTQ
... I'm not aware that it is, just that it will be in the above form - that is taken from an initial run with some known other samples so I can get familiarised with the format and develop pipelines before it arrives. ...
written 11 weeks ago by graeme.thorn • 40
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Comment: C: How do I download TCGA SNV data for patients with ER+/HER2- breast cancer?
... Thanks! I managed to get some of it out of cBioPortal too, but I aggregated enough together to get what I needed to. ...
written 11 weeks ago by graeme.thorn • 40
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Formating RNA-seq with UMIs in unmapped BAM files to UMI-tools compatible FASTQ files
... I'm about to take delivery of large numbers of unmapped (demultiplexed) BAM files from a BGI sequencer with pairs of reads in the following form: A1 77 * 0 0 * * 0 0 RG:Z:rL1 RX:Z:GCGCCCC QX:Z:B(,:.)' BC:Z:GTCTAAACAG QT:Z:.',(/-+*;& A1 141 * 0 0 * * 0 0 RG:Z:rL1 RX:Z:GCGCCCC QX:Z:B( ...
pre-processing umi rna-seq written 11 weeks ago by graeme.thorn • 40
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How do I download TCGA SNV data for patients with ER+/HER2- breast cancer?
... As per the question above, I want to download variation data for ER+ HER2- patients only from the TGCA. There is no option to facet in the GDC Data Portal to get these patients only, and I don't want to have to download all the data from the 1000+ patients and filter them afterwards if I don't have ...
tcga snp written 12 weeks ago by graeme.thorn • 40 • updated 12 weeks ago by Kevin Blighe ♦ 43k
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Answer: A: Filtering IonTorrent variant caller VCFs
... For future reference, what I did was to filter the data using the GATK guidelines on strand bias and read depth and on allelic fraction and quality. DNA damaged during the fixing process is likely randomly distributed, so will have low allelic fraction and low quality as estimated by the variant cal ...
written 12 weeks ago by graeme.thorn • 40
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Comment: C: Filtering IonTorrent variant caller VCFs
... I've got QUAL and AF in both FORMAT and INFO fields. I suspect that damaged DNA has low allelic fraction (there'll be lots of reference reads and not many variant reads) so a filter on the allelic fraction and on quality will remove most of the damaged DNA from the sample. Other filters I applied we ...
written 12 weeks ago by graeme.thorn • 40
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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 4 months ago by graeme.thorn • 40

Latest awards to graeme.thorn

Popular Question 16 days ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 12 weeks ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 7 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 8 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar 10 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 20 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 3.5 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
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