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7

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 raw fast5 data and repeat the basecalling. There is no need to gunzip the fastq.gz prior to alignment. Your commands for alignment look alright, except that (if ...


7

Assuming the read name lines only contain things like @JQ714243-920-1 and nothing else, then sed -i '1~4 s/-[12]$//' file.fastq (N.B., example updated a bit for safety, thanks to @terdon) will remove the -1 and -2 suffixes. However, you should try to figure out why the read names were munged into that form to begin with (at least Illumina machines won't ...


5

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 working on GWA data, you can proceed as follows: for chr in $(seq 1 22) ; do plink --file example --chr $chr --recode --out example_chr$chr ; done You will obtain ...


5

You're using version 1.68 or older. Mauve support was added in 1.70.


5

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 the result into cooler cload pairs should do the trick. gzip -dc GSE109344_monkey_fibro_allValidPairs.txt.gz | cooler cload pairs -c1 2 -p1 3 -c2 5 -p2 6 /data/chromInfo.rheMac2. simple.txt:${...


4

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 initial correction using nanopore-only reads. This will make sure that the best results are obtained from the nanopore signal. First, make sure that the reads ...


4

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 sequencing, metagenomics etc. Please study our papers if you want more details. Reference Standards For Next-Generation Sequencing by Hardwick should be a good ...


3

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 on the issue page. In principle you should be able to do this, it's just a deepTools limitation. This should work fine with computeMatrix, though keep in mind that you're just going to get a big ...


3

It depends of course on your available RAM on your computer. Under Windows you can increase the available RAM in R with memory limit: > memory.limit() [1] 8070 > memory.limit(size=10000) [1] 10000 > memory.limit() [1] 10000 But that is not necessary on linux/unix.


3

The path of least resistance is probably to run the software inside a container. If you install docker, you can just do the following: git clone https://github.com/muccg/docker-blasr.git docker-blasr/bin/blasr (this worked for me on OSX 10.11.6)


3

This is non-parametric statistics, the mean requires confirmation to the normal distribution (but there are exceptions), or perhaps better put it requires a fixed relationship between mean and standard deviation. Non-parametric stats always use the median and are distribution free. Wilcoxon test/ Mann-Whitney U test are used to replace t-test. The Kruscal-...


3

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 that place in the genome, whether the underlying sequence is correct is another question all together. For long nanopore reads, sequence quality is not well ...


2

You might prefer to run VEP in offline mode: Using --cache (without --offline) uses the local cache on disk to fetch most annotations, but allows database connections for some features (see cache limitations) If you need HGVS names in your output, you'll also need to supply a FASTA file using --fasta: --offline Enable offline mode. No database connections ...


2

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 seems to test for correctness or validity of measures of variables. Apparenty, the measurement theory is meant for checking validity of data - the difference ...


2

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/Parasol_job_control_system#SSH_keysssh key setup


2

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 for all the lines that you have it. There should be six lines to correct in this way . You can find an explanation of why here, that tells that the function defined: Returns a Boolean value telling whether EXPR has a value other ...


1

A PDB file has strict spacing rules as documented here. The coordinates should be: 31 - 38 Real(8.3) x Orthogonal coordinates for X. 39 - 46 Real(8.3) y Orthogonal coordinates for Y. 47 - 54 Real(8.3) z Orthogonal coordinates for Z. So trying this on your line: 'HETATM 1 C UNL 1 52355....


1

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, but it looks like it is using zsh. I think that zsh only fairly recently became the standard OSX shell. I don't know the tool or the shell very well, but it ...


1

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

is there reason why you want to compile it by your own? You can install blasr though homebrew and brewsci/science tap : brew tap brewsci/science brew install blasr


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