User: dario.garvan

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dario.garvan460
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Posts by dario.garvan

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Extract RNA Support for Somatic SNV Identified using DNA
... Indeed, `bcftools pileup` with option `-a INFO/AD` is producing the summaries I'm interested in seeing. ...
written 8 weeks ago by dario.garvan460
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Comment: C: Extract RNA Support for Somatic SNV Identified using DNA
... Many studies suggest that a specialised analysis is required for identifying variants using RNA data. So, I would like to avoid using yet another variant calling tool and simply extract the supporting read numbers directly from the BAM files. ...
written 8 weeks ago by dario.garvan460
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Extract RNA Support for Somatic SNV Identified using DNA
... I have a data set which has adjacent normal and tumour samples for both DNA and RNA molecules of cancer patients. Somatic variants have been called using the pair of DNA samples for each patient. I am interested in reporting only the variants which have support by RNA: Each variant has consequence ...
dna and rna integration snv written 8 weeks ago by dario.garvan460
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Answer: A: Why are there many reads with green color in IGV of RNA-seq data?
... One possible explanation is [chromothripsis][1]. There is nothing wrong about mapping RNA-seq reads using TopHat 2, but it's an old method and there are many newer and better methods you could be using. A recent [benchnarking study][2] found that it is one of the worst-performing RNA-seq aligners. ...
written 11 months ago by dario.garvan460
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Answer: A: how to deal with batch effect in TCGA RNA-seq dataset
... TCGA doesn't provide much useful information for doing quality control. You won't be able to input known batches. Another good approach is to use housekeeping genes as controls that should be made more similar between samples. [RUVSeq][1] has functions for estimating batch effects with such genes or ...
written 14 months ago by dario.garvan460
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Comment: C: Clumpify Input via Process Substitution
... Yes, because I made a reduced example which has 1000 reads in each file to test out different approaches. I am using 512 GB RAM and multiple threads on actual data. ...
written 14 months ago by dario.garvan460
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Answer: A: Clumpify Input via Process Substitution
... If there's a lot of extra space on the computer's scratch directory, the easiest to read code would be. cat ${R1[@]} > /scratch/projectID/Patient1_merged_R1.fastq.gz cat ${R2[@]} > /scratch/projectID/Patient1_merged_R2.fastq.gz clumpify.sh -Xmx1g t=1 in1=/scratch/projectID/Patient ...
written 14 months ago by dario.garvan460
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Comment: C: Clumpify Input via Process Substitution
... It's a good answer, but adds an additional software to the pipeline, increasing the future maintenance. ...
written 14 months ago by dario.garvan460
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Comment: C: Clumpify Input via Process Substitution
... I've chosen this as the best answer because it doesn't create extra dependencies. ...
written 14 months ago by dario.garvan460
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Comment: C: Clumpify Input via Process Substitution
... After your suggestion, I did. However, the error remains the same. ``` $ java -ea -cp /usr/local/bbmap/37.98/current/ clump.Clumpify in1=<(cat ${R1[@]}) in2=<(cat ${R2[@]}) out1=$R1output out2=$R2output dedupe subs=1 ``` again produces ``` Starting cris 0. Exception in thread "main" java.la ...
written 14 months ago by dario.garvan460

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For Fixing Encode Rna-Seq Fastq Files
Scholar 4.2 years ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
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