User: agoel

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agoel30
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New User
Location:
UK
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2 months, 2 weeks ago
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4 years, 2 months ago
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m********@gmail.com

Posts by agoel

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Matlab step error in RNA-mutect pipeline
... Thanks, I will drop an email after waiting a bit more. and I will also try if I can implement the filtering steps on my own, though even if I succeed I won't be able to say I used RNA-mutect technically as the actual implementation is hidden to me in the binary script. I will make an effort though a ...
written 3 months ago by agoel30
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Matlab step error in RNA-mutect pipeline
... Hi, I am trying to run [RNA-Mutect][1] and have reached the filtering step (step 2 in the Readme). This step involves calling matlab binary script file and I am repeatedly getting the error detailed below. Hoping to resolve this, I have tried these steps already - 1) Using the pass calls only in t ...
matlab rna-mutect written 3 months ago by agoel30
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Answer: A: trimmomatic 0.36 error
... Is there a file in your current working directory named "trimmomatic-0.36.jar"? If not, you need to provide the full path to that .jar file. ...
written 19 months ago by agoel30
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Answer: A: RealignerTargetCreator inputs multiple Bams??
... For using multiple bam files as inputs to RrealignerTargetCreator, you can use "-I input1.bam -I input2.bam -I input3.bam" in the command. ...
written 3.2 years ago by agoel30
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Comment: C: No positive results after SAM
... Apologies, I mistook this for question on rna-seq. ...
written 3.2 years ago by agoel30
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Answer: A: No positive results after SAM
... You can learn from here [limma][1] .Good example ! [1]: http://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html ...
written 3.2 years ago by agoel30
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Comment: A: Trimmomatic adapter file TruSeq3-PE-2.fa
... You can use cutadapt [link][1]. Might be useful for you. [1]: http://cutadapt.readthedocs.io/en/stable/guide.html#illumina-truseq ...
written 3.2 years ago by agoel30
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Answer: A: comparing phylogenetic trees
... Have a look. Might be useful for you.[Compare PhylogeneticTrees][1] [1]: https://www.biostars.org/p/6912/ ...
written 3.3 years ago by agoel30
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Platypus based joint variant calling
... Hi, I am trying to use [Platypus][1] to get joint variation calling on >200 BAM files (tumour/normal tissue samples. Avg. depth of cov. is 80x).I am assigning 8 processors and have 32Gb RAM available. When I try with a couple of samples, Platypus runs fine. But with all samples, it gets stuck. T ...
software error exome variant calling written 3.3 years ago by agoel30
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Answer: A: Can we do between-sample normalization like deseq/TMM on RPKM?
... RNA-seq expression values can be enumerated by two methods - Count-based or, RPKM/ FPKM based In the case of the latter, the values are estimates and hence in decimals. Since they are in decimals, robust statistical procedures aren't available to them. Whereas, Count-based data are whole numbers (s ...
written 3.4 years ago by agoel30

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Popular Question 17 months ago, created a question with more than 1,000 views. For Platypus based joint variant calling
Supporter 3.0 years ago, voted at least 25 times.

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