User: dodausp

gravatar for dodausp
dodausp140
Reputation:
140
Status:
Trusted
Location:
Denmark/Copenhagen/BRIC
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 10 months ago
Email:
d******@gmail.com

Posts by dodausp

<prev • 60 results • page 1 of 6 • next >
1
vote
2
answers
7.1k
views
2
answers
Comment: C: Best tool for variant calling
... Hi, @Kevin Blighe I'm just adding a small contribution here, because I am now trying to understand how DeepVariant works: couldn't find any reference about its benchmarking in clinical genetics, but I came across this comparison study: [DeepVariant x GATK4 x SpeedSeq](https://www.nature.com/articles ...
written 3 months ago by dodausp140
0
votes
0
answers
146
views
0
answers
Comment: C: Retrieving multiple regions (from a list) in a bam file and outputing as a table
... I would like to extract the sequence of the *bam* file; it is, the consensus sequence of the given *bam* file. ...
written 6 months ago by dodausp140
0
votes
0
answers
146
views
0
answers
Retrieving multiple regions (from a list) in a bam file and outputing as a table
... Hi there! First of all, I hope all are safe and taking the necessary precautions amid this covid-19 situation. Now, to my question, say I have a list (or a data frame) file with regions of interest like this: Chromosome start end 1 chr1 8827004 8827026 2 chr1 ...
data frame wes snp written 6 months ago by dodausp140
0
votes
0
answers
164
views
0
answers
Comment: C: Run RNA-seq analysis with selected targets
... Thank you @ATpoint. I agree with you, having the raw data gives one more flexibility and control over the data. The issue however is that it was retrieved from a data bank repository, with restricted access. And the only type of data we have access to are those `bam` files, **already pre-processed i ...
written 7 months ago by dodausp140
1
vote
0
answers
164
views
0
answers
Run RNA-seq analysis with selected targets
... I have obtained a considerable large amount of data (~750 samples) from a collaboration study to perform RNA-seq analysis. The data is not raw, and by inspecting the files and some metadata, here is some information gathered: - the file sizes range from a few MB to a couple of GB; - all files hav ...
alignment cufflinks rna-seq written 7 months ago by dodausp140
0
votes
0
answers
143
views
0
answers
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 7 months ago by dodausp140
1
vote
1
answer
183
views
1
answers
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 7 months ago by dodausp140
2
votes
1
answer
183
views
1
answer
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 7 months ago by dodausp140 • updated 7 months ago by Barry Digby460
0
votes
2
answers
1.3k
views
2
answers
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 8 months ago by dodausp140
0
votes
0
answers
163
views
0
answers
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 8 months ago by dodausp140

Latest awards to dodausp

Popular Question 4 months ago, created a question with more than 1,000 views. For NMF not working for identifying mutational signature
Popular Question 6 months ago, created a question with more than 1,000 views. For How to set the control group in microarray analysis from illumina data?
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Supporter 16 months ago, voted at least 25 times.
Popular Question 20 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 21 months ago, created an answer with at least 3 up-votes. For A: Drug interaction not running in MAFtools
Scholar 21 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Scholar 21 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Popular Question 23 months ago, created a question with more than 1,000 views. For Biobase not running in R 3.5.0

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1785 users visited in the last hour