User: graeme.thorn
graeme.thorn • 30
- Reputation:
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- Location:
- London, United Kingdom
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 3 years, 2 months ago
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Posts by graeme.thorn
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... 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 9 weeks ago by
graeme.thorn • 30
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... 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 9 weeks ago by
graeme.thorn • 30
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... 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 ...
written 10 weeks ago by
graeme.thorn • 30
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... 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 4 months ago by
graeme.thorn • 30
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... 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 4 months ago by
graeme.thorn • 30
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... I want to download RNA-seq and mutation data from the ICGC data portal at https://dcc.icgc.org/, but I'm only interested in triple negative breast cancer patients. Is there a quick and easy way to either filter the portal to get only the TNBC data, or a quick way to classify the data once downloaded ...
written 4 months ago by
graeme.thorn • 30
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... Thanks to another question on Biostars: https://www.biostars.org/p/313063/, I have found an accessible link to a translation table: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables.
...
written 4 months ago by
graeme.thorn • 30
3
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... I have downloaded some RNA-seq and mutation data from the TGCA (legacy) portal. I want to be able to identify which samples have both normal and tumour.
As far as I can tell (from other questions), the last section of the 4-part barcode (TCGA-##-####-***) is the tissue identifier.
However, the lin ...
written 4 months ago by
graeme.thorn • 30
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... I have a long BED-like file generated by bedtools intersect which has the following form:
chr1 1 100 chr1 1 10 0.9
chr1 1 100 chr1 11 20 0.5
chr1 1 100 chr1 21 30 0.92
....
chr1 1 100 chr1 91 100 0.3
chr1 101 200 chr1 101 110 0.3
....
chr1 101 200 ...
written 14 months ago by
graeme.thorn • 30
• updated
14 months ago by
Pierre Lindenbaum ♦ 115k
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... And, of course, this would work if the BED files have more than three columns, just change the printf(".\t-1\t-1\n"); to include more fields. ...
written 14 months ago by
graeme.thorn • 30
Latest awards to graeme.thorn
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: Error in GSNAP - unable to find genome in directory
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar
4 months ago,
created an answer that has been accepted.
For A: Error in GSNAP - unable to find genome in directory
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Error in GSNAP - unable to find genome in directory
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: Error in GSNAP - unable to find genome in directory
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