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8 votes
Accepted

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

Insertions and deletions are the dominant error mode of long read sequencing, including nanopore sequencing. What you see is not unexpected. Things may have improved by now if you would download the ...
Wouter De Coster's user avatar
7 votes
Accepted

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

Assuming the read name lines only contain things like @JQ714243-920-1 and nothing else, then sed -i '1~4 s/-[12]$//' file.fastq (...
Devon Ryan's user avatar
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5 votes
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Using SED command in Nextflow script

Inside your script's command string, assembly_id is actually a java.lang.String so trying to manipulate it with a Bash operation (i.e. using ...
Steve's user avatar
  • 3,109
5 votes
Accepted

cooler out of memory

It seems to be some kind of a memory leak in pandas's read_csv, maybe due to it doing gzip-decompression. Doing the decompression in a separate process and piping ...
nvictus's user avatar
  • 166
5 votes
Accepted

problem of "ordering in physical positions" phasing SNPs with Shapeit

The manual suggests that each "chromosome" needs to have its own input file. You have to split the dataset by chromosomes. ShapeIT can just phase one chromosome at a time. If you are ...
Bioathlete's user avatar
  • 2,574
5 votes
Accepted

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

You're using version 1.68 or older. Mauve support was added in 1.70.
Devon Ryan's user avatar
  • 19.6k
4 votes
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checks for spike-in sequence controls

Disclaimer: I'm a developer for http://www.sequin.xyz. Sequin is a new set of spiked-in controls for next-generation sequencing, and that includes Illumina. We design controls for RNA-Seq, genome ...
SmallChess's user avatar
  • 2,709
4 votes
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What are some ways to error correct Oxford Nanopore long read sequencing?

How are you evaluating sequencing error rate? My most recent re-calls of 2017 sequences are demonstrating median single-read accuracy over 96%. Before considering Illumina, it'd be worth it to do an ...
gringer's user avatar
  • 14.3k
4 votes

Nextflow with Minimap2 not working

Command error: .command.sh: line 2: ./minimap2: No such file or directory Work dir: /Users/rimo/Desktop/AWS/minimap2/work/ae/47e3c0708f33b1949315fc83066b95 ...
Steve's user avatar
  • 3,109
3 votes
Accepted

Process gets killed before completing

You've overloaded the memory. One route is to deploy "chunking". pandas will do this. This is complicated to implement code wise however. My suggested solution (because it simpler) would be ...
M__'s user avatar
  • 12.6k
3 votes
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KeyError '/n' in Bio SeqUtils Package ProtParam Script

When the user is pushing enter on their keyboard, it is likely inserting a newline character (\n) at the end of the user input <...
JamesT's user avatar
  • 191
3 votes

Difference between clinical significance and statistical significance

This is non-parametric statistics, the mean requires conformation to the normal distribution (but there are exceptions), or perhaps better put it requires a fixed relationship between mean and ...
M__'s user avatar
  • 12.6k
3 votes

Oxford Nanopore mapping Quality and sequencing error

Where i know with the phred score mapQ of 60 means 99.9999% of the bases are called correctly. That's not at all what the MAPQ means, it means that the sequence is very likely to have originated from ...
Devon Ryan's user avatar
  • 19.6k
3 votes
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Dealing with absence of coverage

I'll fix the bamCoverage issue in the 2.6.0 release (it may already be fixed since I rewrite how bigWig files are made for that release). You can follow my status ...
Devon Ryan's user avatar
  • 19.6k
3 votes
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GFF file too big to load into R

It depends of course on your available RAM on your computer. Under Windows you can increase the available RAM in R with memory limit: ...
benn's user avatar
  • 3,581
3 votes
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How to install blasr on Mac OS X?

The path of least resistance is probably to run the software inside a container. If you install docker, you can just do the following: ...
heathobrien's user avatar
  • 1,816
2 votes

How to install blasr on Mac OS X?

I've had many issues with installing blasr on my own, but it's a breeze using (bio)conda, see https://anaconda.org/bioconda/blasr conda install -c bioconda blasr
Wouter De Coster's user avatar
2 votes
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Difference between clinical significance and statistical significance

Another viewpoint could be : statistically significant implies use of sampling theory to establish presence of significant difference between case and control groups. The "clinical " significance ...
Subhash C. Davar's user avatar
2 votes
Accepted

Accessing UCSC genome via ssh results in a validation error

You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys: http://genomewiki.ucsc.edu/index.php/...
Null Model's user avatar
2 votes
Accepted

the following errors are found during the installation of an open source software, UNCeqR on z shell

It is a Perl compilation error: (Perl libraries) Math::CDF-0.1 -- Generate probabilities and quantiles from several statistical probability functions conda install -c bioconda perl-math-cdf cpan ...
envs_h_gang_5's user avatar
2 votes

Ensembl Variant Effect Predictor (VEP) issue during execution

You might prefer to run VEP in offline mode: Using --cache (without --offline) uses the local cache on disk to fetch most ...
Steve's user avatar
  • 3,109
2 votes

MUMmer plot error. Line 884. What to do?

I had the same error and I solved by removing defined and writing only if (%$rref) in the mummerplot code. You have to do this ...
HelpNeederStudent's user avatar
2 votes
Accepted

Nextflow Pipeline: Unexpected Input "{"

Nextflow does not have an env process directive. If stringtie is not already in your $PATH, ...
Steve's user avatar
  • 3,109
2 votes

ValueError: count not convert string to float

Ah! I finally got it to work! I used your command but I had to change it up a little bit to work with my data. The final command I used is this: ...
rimo's user avatar
  • 1,003
1 vote

MEGA11 gives the error "stop codons are found in the translated sequences", even though there are not!

The solution is very simply, MegaX will not allow any stop codons within the "translated" sequence. The reason is simple MEGAX's function is phylogenetic models with nucleotide or protein ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

ValueError: count not convert string to float

The following would be useful, print (heterozygosity_df.columns) This looks like static typing issue within pandas. What I suspect is ...
M__'s user avatar
  • 12.6k
1 vote

Pairwise alignment using CIGAR String

Following the basic rules and preferring the AAG contiguous we can write: 01234 AAGCT (ref) AAAAGGC (query) So the ...
GavinBrelstaff's user avatar
1 vote

Error pasing the following line in pdb

A PDB file has strict spacing rules as documented here. The coordinates should be: ...
Matteo Ferla's user avatar
  • 4,244
1 vote

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

This is a tough one, because the only relevant lines from your GSEA debug log were these two: ...
Kevin E's user avatar
  • 111
1 vote

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

It is possible that the shell being used in the process is different from your standard command line shell. I am not familiar with the tool, and it's hard to say more without knowing your OSX version, ...
Maximilian Press's user avatar

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