elcortegano
elcortegano
Hi, I'd like to use circlator to assembly a mitochondrion genome. I have (PacBio) reads and "linear" contig-level assemblies for a number of samples, as well as a different "reference"...
Hi, manta is returning an error that cannot open a file (that exists), but that I think might relate to the number of samples used, or probably something else. When...
`unimap` does a great job aligning complex regions (e.g. satellites) even using reads. We are using it to detect some variants at telomeric regions, using PacBio HiFi sequencing data. We...
I'm using sniffles (more specifically I did use the old version v1.0.12b), and when running it we excluded non-primary alignment reads from the BAM files (using `samtools view -F 256`)....
Hi, we have noted that assemblies generated with Flye very frequently introduce variants that are not supported by the reads, particularly at highly repetitive regions (but also in others as...
The END block of `awk` does not check whether the NR variable is NULL or not, which sometimes results in "fatal: division by zero attempted" errors. The code changes prevent...
In many instances, no deletions or insertions are present in blast files, resulting in errors reported by `cat` and `rm`. For example: ``` cat: test.deletion_blast: No such file or directory...
I am running `gatk GenotypeGVCFs` and want to get output for all genomic sites. I was expecting the output to include parameters like QUAL and mapping quality (MQ) for invariant...
I'm having issues with a large genome (2.7 Gb) sample, and I think the script might actually be stuck. It's been running for about two weeks now, with no output...
Following a recent issue open in the IGV site (https://github.com/igvteam/igv/issues/1303), we wonder if `aligned_bam_to_cpg_scores.py` would call 5mC methylated CpG sites at insertions (i.e. at sites that are not in the...