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Questions tagged [errors]

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I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application

I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would ...
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0answers
15 views

I am getting a parsing error when uploading .chip file to GSEA software

I get the following error when I try to load a .chip file to GSEA software. What is the problem? ...
4
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1answer
165 views

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

I'm a starting my analysis on nanopore whole genome sequencing. I start my analysis from this popular Github. The sample I downloaded was WGS for NA12878, so I would assume it's alignment to GRCh38 ...
4
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1answer
53 views

Script Giving error at paste command

I wrote script for pasting rsids on CADD output. Here is script. ...
2
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0answers
25 views

hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
1
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1answer
44 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
1
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1answer
63 views

GFF file too big to load into R

I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome. I used the following code: ...
0
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1answer
38 views

Error while Importing fastq sequences to jMHC software

I am trying to analyze my .fastq files (MiSeq exon reads) with the jMHC software, but output files I have obtained have no results. I think I might be doing something wrong during the first step: "...
0
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3answers
160 views

How to install blasr on Mac OS X?

I am trying to install blasr on mac osx. I followed the steps here I get the error below after using the 'make' command: ...
3
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1answer
174 views

Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?

On this Biopython tutorial, they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module: ...
6
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1answer
696 views

Is there a more elegant solution to the bwa-mem: paired reads have different names error?

I'm currently trying to run bwa-mem on Influenza substrains using the following command: ~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq h5n1_1_cons.fa ...
3
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1answer
160 views

problem of “ordering in physical positions” phasing SNPs with Shapeit

I'm trying to phase my data (whole genome resequencing SNPs) with Shapeit (from ped file) and I get this error message : ...
5
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1answer
88 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
6
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1answer
88 views

checks for spike-in sequence controls

I would like to know what do people verify when designing/using spike-in controls, to be used in sequencing experiments (mainly Illumina). So far I came up with this list: Does it align only to a ...