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Questions tagged [errors]

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2
votes
0answers
12 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
vote
1answer
38 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 ...
0
votes
1answer
54 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
votes
1answer
37 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
votes
3answers
142 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
votes
1answer
151 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
votes
1answer
514 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
votes
1answer
123 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
votes
1answer
81 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
6
votes
1answer
67 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 ...