Newest Questions
6,549 questions
3
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How can I group mitochondrial heteroplasmy into bins based on age
I have mitochondrial heteroplasmy data obtained from ddPCR that I am trying to group into age bins. One bin edge has to be 0. I would like to dynamically choose all the other bin edges.
Each bin ...
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1
vote
0
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35
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Hard Filtering Differences between WES and WGS
I am working on human WGS data and i need to detect SNPs and INDELs, during the variant calling step i have to use a filter to remove false SNPs or in general bad quality SNPs, i am wondering if I ...
1
vote
1
answer
59
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How can I visualize read depth from sequencing data?
This question was also asked on Biostars
I am currently on a genomic variants analysis and have completed the alignment step (BQSR and Apply , depth sequencing....). If any of you can help me or ...
1
vote
1
answer
40
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Install DCA and its dependencies
I am trying to install DCA but it fails due to dependency issues. The package is no longer being maintained. Following are the commands I need to run:
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2
votes
1
answer
23
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Reference genome masking reason for particular position
I'm trying to use an alignment tool like BLAST (in fast LAST) with the hg19 masked genome, but it is failing to find a sequence at a particular location, and I've determined that it is due to the ...
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2
votes
1
answer
53
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How and why do alignment algorithms work?
I'm majoring in life sciences. I just started a course in bioinformatics, and this is my first time diving into this topic. (No prior CS background/bioinfo background).
First, when we align two ...
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2
votes
1
answer
20
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How can I fix an igraph produced by Fella package?
I need to ask a question about Fella package: I have used this package for pathway analysis and I created this graph with this code as instructed in its vignette, but the graph is not clear and the ...
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2
votes
1
answer
46
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vcf GT fields meaning and how to extract
I have an issue to understand the whole meaning of a vcf from a genome in a bottle project. Here is one line of this file for the two fields of interest (only the format and sample fields):
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1
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1
answer
29
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affy::rma results doesn't match with ncbi website
I'm trying to find out how RMA normalized signal intensity values in this sample have been calculated. I tried to perform RMA in R, but the results are different
<...
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1
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0
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28
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How to reshape a data frame in R without aggregation and create a heatmap?
I have dataframe data that looks like below:
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1
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0
answers
28
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What is the best approach for comparing .bed Files from nf-core/chipseq workflow for Venn Diagram creation?
I recently used the nf-core/chipseq workflow to analyze ChIP-seq data for the same protein across different cell types. Now, I must create a Venn diagram to compare ...
1
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0
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66
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PacBio lima fails to rename files during demultiplexing
I've got some PacBio multiplexed amplicon sequencing data that I'd like to use lima to demultiplex. I also want to rename the resulting files based on the barcode combination using a biosample.csv. I ...
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1
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0
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5
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clusterMaker2 installation on cytoscape 3.10.3: functionality not enabled
I have installed clusterMaker2 on cytoscape 3.10.3 but when trying to use the app all the functionality is not enabled. For example cannot select clusterMaker cluster attributes since the selections ...
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2
votes
2
answers
72
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Variant calling on amplicon sequencing data
I've got some human amplicon sequencing data which I know contains variants, but I'm trying to work out the best way to call the variants, as most variant callers seem set up for whole genome data. I'...
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1
vote
2
answers
87
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deepvariant fails on nanopore long read amplicon sequencing data
I've got some human Oxford Nanopore long read amplicon data which I know contains variants, but can't get deepvariant to work.
The amplicon is at chr15:30904775-30905567, and you can see the indexed ...
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