desmodus1984

POLCA error ufasta-variant calling.

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Hi, I build an assembly using long-reads and now I want to polish it using POLCA. At first, I didn't specify the $PATH to bwa, but fixed it, then had...

Hi, I tried to install the latest version and I got the following error/warning messages. Please let me know if they are important, and/or what should I do to fix...

Hi, I would appreciate if you can help me. I am interested in demographic inference of bats. I assembled a reference genome, and I have downloaded mouse and human X...

Error with download_eggnog_database.py

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Hi, I am trying to follow the instructions on the website for doing the annotations and I would appreciate some help. I am an amateur but trying to learn. I...

Hi, I am interested in trying strelka because I have been trying GATK but it takes a ridiculously large time for variant calling. I downloaded and unzipped the binary distribution...

Bcftools error -filtering error: the tag "\" is not defined in the VCF header

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Hi, I have genotyped a group of samples and then I used bcftools to exclude one which had a lot of missing data. I used the following code to do...

Protein: OrthoDB enough or get sequences from sister species

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Hi, I am planning the annotation of a bat genome. For scaffolding I used the reference genome of sister species. I am unsure whether it would be sufficient to use...

Hi, I am trying to assemble a genome of ~2.5 GB with ~15X of Nanopore data and ~65X of 100bps short-read data. I did one run of Abyss and I...

Job using merged read pairs and unmerged read pairs gets killed

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# Please report - [ ] version of ABySS with `abyss-pe version` abyss-pe (ABySS) 2.3.5 - [ ] distribution of Linux with `lsb_release -d` Red Hat Enterprise Linux Server release...

Test - error report - 0 corrected reads?

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Hi, I sequenced a genome and I got 16 paired-end libraries. To test the speed of the program, I picked on library ~11 Gb each .gz file, and used the...