User: dodausp

gravatar for dodausp
dodausp130
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130
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Denmark/Copenhagen/BRIC
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4 days, 5 hours ago
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4 years, 3 months ago
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Posts by dodausp

<prev • 55 results • page 1 of 6 • next >
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RNA-seq assembly data not matching reference (cufflinks)
... Hi! I have recently posted a [question](https://www.biostars.org/p/420308/) on this matter, but this one is quite a different issue. I am using cufflinks to quantitate my RNA-seq data. And in order to get the gene names, the ```-g``` argument is enabled, with the proper ```gtf``` [reference](http:// ...
assembly alignment rna-seq written 10 days ago by dodausp130
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Comment: C: How to perform iteration task inside a docker image (RNA-seq analysis)
... Thanks a lot, @Barry Digby! That's the first time I heard about nextflow. I will definitely give it a go and post a follow-up here. Many thanks again! ...
written 11 days ago by dodausp130
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How to perform iteration task inside a docker image (RNA-seq analysis)
... Hi, there I am using [docker](https://docs.docker.com/) containers to run a pipeline for RNA-seq analysis. Specifically, I am using [cufflinks](https://biocontainers.pro/#/tools/cufflinks) now, to quantitate and annotate the transcripts. I am dealing with 770 .bam files (aligned by TopHat), and run ...
quantification docker rna-seq written 11 days ago by dodausp130 • updated 11 days ago by Barry Digby290
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Answer: A: error while running vcf2maf
... I was running *vcf2maf* on Linux and came across the same problem. So, my question is: **are you running it on Linux as well?** If so, it seems that this is a matter of [line break system in different OS][1]. Fortunately, that can be easily fixed by ```dos2unix``` command. In my case, I ran: ``` d ...
written 5 weeks ago by dodausp130
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Comment: C: How to compare sequencing data from same sample, but from different methods?
... Thanks, @ATpoint. I see there is even a [handful of comparisons][1] between these two plot methods. I will definitely try to apply it to the analysis. I think it will be useful to show how many elements (variants) are common between the groups. I was also thinking about showing the elements that are ...
written 6 weeks ago by dodausp130
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How to compare sequencing data from same sample, but from different methods?
... Hi! There are actually 2 similar situations for the same question, but it might be better to explain the design of each first: 1. With a small cohort of 16 samples (from patients), we would like to compare the output of our standard variant calling pipeline (fully automated, by IonTorrent) with an ...
comparison sequencing written 6 weeks ago by dodausp130
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Comment: C: How to use ExAC/gnomAD without chrN_random?
... I tried, and unfortunately it did not work @Pierre Lindenbaum. I did come up with something else that solved the problem, though (explained below). Thanks a lot for the suggestion! (: ...
written 9 weeks ago by dodausp130
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Answer: A: How to use ExAC/gnomAD without chrN_random?
... Case solved. Basically, I liftedOver the ExAC file to the *hg19* build used on our sequecing platform (*hg19* without those chrN_random annotations), and arranged it so gatk's ```GetPileupSummaries``` could interpret it. In case anybody comes across that, here are the steps: **1. LiftingOver ExAC ...
written 9 weeks ago by dodausp130
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Comment: C: How to use ExAC/gnomAD without chrN_random?
... Thanks a lot, @Pierre Lindenbaum! (: Trying that right now. Will post an update later. ...
written 9 weeks ago by dodausp130
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How to use ExAC/gnomAD without chrN_random?
... Hi, I am trying to estimate my sample contamination based on gatk's ```GetPileupSummaries / CalculateContamination``` [best practices](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11146). This pipeline requires a *.vcf* file containing common germline variant sites, which her ...
variant calling exac snp sequencing written 9 weeks ago by dodausp130

Latest awards to dodausp

Scholar 9 weeks ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Supporter 9 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For How to set the control group in microarray analysis from illumina data?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Drug interaction not running in MAFtools
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Popular Question 16 months ago, created a question with more than 1,000 views. For Biobase not running in R 3.5.0

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