User: vegard nygaard

gravatar for vegard nygaard
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170
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Trusted
Location:
Oslo University Hospital, Norway
Last seen:
2 years, 5 months ago
Joined:
3 years, 9 months ago
Email:
v*************@medisin.uio.no

Posts by vegard nygaard

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Contamination of human DNA in genome sequencing data. How to detect and eliminat
... You aim to use conpair in a way it was not intended. To clarify, "normal sample" in a cancer setting means non-cancerous cells from the same patient. So conpair uses blood and tumor, both from the same patient. If you provide your technicians DNA as normal and a patients DNA as "tumor" conpair will ...
written 2.5 years ago by vegard nygaard170
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Comment: C: Contamination of human DNA in genome sequencing data. How to detect and eliminat
... We have used conpair https://github.com/nygenome/Conpair for cancer samples. I think it requires a normal sample as well, so it might not work your your task. At least, It was able to detect 2% contamination fairy well, but it might depend on read depth and number of SNPs included. This tool does n ...
written 2.5 years ago by vegard nygaard170
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Answer: A: Expression data missing in a GEO study
... I found this old unanswered post while troubleshooting. I had the same problem for some other GEO data sets (GSE46691, GSE79956, GSE79957, GSE62667). The explanation, given by GEO-support, for the missing data is that the file accessed by getGEO ("series_matrix" or "soft" in the GEO record) does n ...
written 2.8 years ago by vegard nygaard170
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Comment: C: Why does stringtie --merge remove potential novel transcript isoforms if they ar
... Thanks for a useful suggestion. I have tried without the reference annotation, however the problem is really the same. A novel transcript will be discarded in the merge step if it is a substring of another transcript (novel or from annotation). I got an answer from the developer [here][1]. It see ...
written 3.5 years ago by vegard nygaard170
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Why does stringtie --merge remove potential novel transcript isoforms if they are substrings of longer isoforms?
... Hi, I am trying the hisat2 -> stringtie -> ballgown workflow. I have 46 samples from 2 tissues. I run stringtie 3 times as described in http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html, approximately like this: stringtie sample1.bam -G genes_ensembl_GRCh37_20150717.gtf -o ...
isoforms rna-seq written 3.6 years ago by vegard nygaard170 • updated 3.5 years ago by dgrover610
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Tool for replacing variant-bases with reference in aligned reads, i.e anonymize bam files?
... Hi, I am looking for a tool that takes as input a bamfile with aligned reads and the reference genome and outputs a bamfile where every variant (non-reference basecall) is replaced with the reference base call, but the alignment is kept. I need this in order to de-senitize bam files so I am allowed ...
rna-seq written 3.6 years ago by vegard nygaard170
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Comment: C: Are we tricking ourselves with batch effect correction?
... We spent considerable time on simulations of the type also described by Neilfws. And as aides in doing so, we made a couple of shiny-tools, "[batch-adjustment-simulator][1]" and the somewhat sparsely documented "[fdist-app][2]", with source code available via our additional analyses page at GitHub; ...
written 3.8 years ago by vegard nygaard170
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Answer: A: Are we tricking ourselves with batch effect correction?
... Hi Christian. I found your post a little late, but I found it so interesting that a will give it a late answer. In your description of your experiment, you do not inform of the experiment design, if the batches contained the same proportion of samples from your biological groups. Based on your ob ...
written 3.8 years ago by vegard nygaard170

Latest awards to vegard nygaard

Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Are we tricking ourselves with batch effect correction?
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Are we tricking ourselves with batch effect correction?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Are we tricking ourselves with batch effect correction?

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