User: bruce.moran

gravatar for bruce.moran
bruce.moran620
Reputation:
620
Status:
Trusted
Location:
Ireland
Last seen:
10 hours ago
Joined:
6 years, 8 months ago
Email:
b**********@gmail.com

about me

Posts by bruce.moran

<prev • 114 results • page 1 of 12 • next >
0
votes
0
answers
284
views
0
answers
Comment: C: Need help understanding ARACNe-AP output
... You need to find 'master regulators' using for example [viper][1] [1]: https://www.bioconductor.org/packages/release/bioc/html/viper.html ...
written 21 days ago by bruce.moran620
0
votes
0
answers
308
views
0
answers
Comment: C: Ploidy for variant calling in tumor pooled samples for amplicon next-generation
... For both MuTect2, HaplotypeCaller (no experience with FreeBayes) > Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). So DNA was pooled, libraries made and sequenced? The four tumours are all from the same individual? Is the amplicon panel only on the ...
written 10 weeks ago by bruce.moran620
0
votes
0
answers
173
views
0
answers
Comment: C: GATK4 VariantRecalibrator resource error
... Don't do much germline mutation calling, but I think ExAC might have superseded HapMap? No idea WRT `-comp`. I highly recommend [the GATK website][1], it's a bit of a mess because of versioning but the users and mods are very active, and because it's GATK your error will have occurred for others and ...
written 3 months ago by bruce.moran620
0
votes
0
answers
173
views
0
answers
Comment: C: GATK4 VariantRecalibrator resource error
... Have a look at [this thread][1] Basically you need a `:` between resource parameters and the resource path: --resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0:/xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf Although this also depends on your version of GATK... [1]: ...
written 3 months ago by bruce.moran620
3
votes
1
answer
195
views
1
answers
Answer: C: Post-filtering WES for mutation calling
... Most GATK tools have the [--intervals (-L) flag][1] which allows you to input a file of the regions that you are interested in, i.e. your exome. That is the stage at which I usually reduce to the region of interest. My rationale is that copy number callers can sometimes use off-target reads from e ...
written 4 months ago by bruce.moran620
2
votes
1
answer
1.3k
views
1
answers
Comment: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... For a conservative estimate, I use non-synonymous mutations, but [the recent MSK-IMPACT paper][1] used all somatic muatations: > Mutational-load assessment and statistical analysis. The total number > of somatic mutations identified was normalized to the exonic coverage > of the respective ...
written 5 months ago by bruce.moran620
2
votes
1
answer
1.3k
views
1
answers
Answer: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... Mutational load is more a population genetics term IIRC, whereas TMB is specific to somatic variants. To calculate TMB, you need to know the total size of the region sequenced. If data is from exome sequencing, you would find the size of the exome capture, and divide total mutations (or non-synony ...
written 5 months ago by bruce.moran620
1
vote
2
answers
341
views
2
answers
Comment: C: Microsatellite Instability, Whole exome sequencing
... Because microsatellites are so highly variable per individual, I think you will need matched normal to test MSI. Without matched normal you could investigate tumour mutational burden (TMB). ...
written 5 months ago by bruce.moran620
1
vote
2
answers
341
views
2
answers
Answer: A: Microsatellite Instability, Whole exome sequencing
... There was a [good editorial][1] on MSI in JCO PO a few years ago, alongside [this paper][2] which references the set of 2,359 microsatellites in or near the exome. So reason is that not all are in non-coding regions. [1]: https://ascopubs.org/doi/full/10.1200/PO.17.00189 [2]: https://ascopubs.o ...
written 5 months ago by bruce.moran620
0
votes
1
answer
473
views
1
answers
Comment: C: low unique mapping ratio of RNA-seq data
... The `samtools view -F 256` command should output primary alignments. The [HiSat2 manual][1] states: > Each reported read or pair alignment beyond the first has the SAM > 'secondary' bit (which equals 256) set in its FLAGS field. You have paired data so it is 81,968,964/2 = 40,984,482 'primar ...
written 5 months ago by bruce.moran620

Latest awards to bruce.moran

Scholar 4 months ago, created an answer that has been accepted. For A: Picard-tools mark duplicates error, missing @RG
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
Popular Question 4 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
Popular Question 5 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
Centurion 6 months ago, created 100 posts.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
Scholar 6 months ago, created an answer that has been accepted. For A: Picard-tools mark duplicates error, missing @RG
Popular Question 10 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
Popular Question 17 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
Popular Question 17 months ago, created a question with more than 1,000 views. For AnnotationDBi for NMF Subtyping of RNAseq
Popular Question 18 months ago, created a question with more than 1,000 views. For Variant Effect Predictor warnings Chromosome 'p' not found in cache
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
Student 22 months ago, asked a question with at least 3 up-votes. For CWL rerunning completed output
Popular Question 22 months ago, created a question with more than 1,000 views. For SIFT command line help (non-human)
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
Scholar 2.1 years ago, created an answer that has been accepted. For A: Picard-tools mark duplicates error, missing @RG
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How To Visualize Splice Junction Data, In Particular Exon-Skipping
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.6 years ago, created an answer that has been accepted. For A: Picard-tools mark duplicates error, missing @RG
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
Popular Question 2.9 years ago, created a question with more than 1,000 views. For What Information Do The Files For The String Protein Downloads Contain.
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Picard Tools Markduplicates 'No Group 1' Error
Scholar 4.2 years ago, created an answer that has been accepted. For A: Picard-tools mark duplicates error, missing @RG
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How To Visualize Splice Junction Data, In Particular Exon-Skipping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1447 users visited in the last hour