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 ...
- 1,464
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 (...
- 19.8k
5
votes
Accepted
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 ...
- 3,287
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 ...
- 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 ...
- 2,584
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.
- 19.8k
4
votes
Accepted
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 ...
- 2,746
4
votes
Accepted
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 ...
- 15.1k
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
...
- 3,287
3
votes
Accepted
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 <...
- 191
3
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 ...
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__♦
- 13k
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 ...
- 19.8k
3
votes
Accepted
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 ...
- 19.8k
3
votes
Accepted
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:
...
- 3,601
3
votes
Accepted
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:
...
- 1,816
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__♦
- 13k
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
- 1,464
2
votes
Accepted
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 ...
- 200
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/...
- 81
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 ...
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 ...
- 3,287
2
votes
Accepted
Nextflow Pipeline: Unexpected Input "{"
Nextflow does not have an env process directive. If stringtie is not already in your $PATH, ...
- 3,287
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:
...
- 1,063
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__♦
- 13k
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 ...
- 111
1
vote
Error pasing the following line in pdb
A PDB file has strict spacing rules as documented here.
The coordinates should be:
...
- 4,274
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:
...
- 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, ...
- 4,252
Only top scored, non community-wiki answers of a minimum length are eligible