User: graeme.thorn

gravatar for graeme.thorn
graeme.thorn40
Reputation:
40
Status:
New User
Location:
London, United Kingdom
Last seen:
15 hours ago
Joined:
2 years, 12 months ago
Email:
g***********@gmail.com

Posts by graeme.thorn

<prev • 16 results • page 1 of 2 • next >
1
vote
1
answer
72
views
1
answers
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 3 days ago by graeme.thorn40
0
votes
1
answer
72
views
1
answers
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 3 days ago by graeme.thorn40
1
vote
1
answer
72
views
1
answer
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 10 days ago by graeme.thorn40
0
votes
0
answers
158
views
0
answers
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 9 weeks ago by graeme.thorn40
0
votes
0
answers
158
views
0
answers
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 9 weeks ago by graeme.thorn40
0
votes
0
answers
158
views
0
answers
Downloading triple negative breast cancer data from ICGC
... 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 ...
icgc rna-seq written 9 weeks ago by graeme.thorn40
3
votes
1
answer
174
views
1
answers
Answer: A: TCGA (legacy) barcodes for identifying tumour/normal samples
... 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 11 weeks ago by graeme.thorn40
4
votes
1
answer
174
views
1
answer
TCGA (legacy) barcodes for identifying tumour/normal samples
... 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 ...
rna-seq written 11 weeks ago by graeme.thorn40
5
votes
2
answers
432
views
5 follow
2
answers
Split bed file by unique first three columns
... 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 ...
bedtools bed split written 12 months ago by graeme.thorn40 • updated 12 months ago by Pierre Lindenbaum112k
0
votes
1
answer
644
views
1
answers
Comment: C: bedtools intersect "complete outer join"
... 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 12 months ago by graeme.thorn40

Latest awards to graeme.thorn

Scholar 3 days ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar 11 weeks ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 12 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 2.8 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1581 users visited in the last hour