darencard / darencard.github.io

Daren Card's professional website

Hey! I'm Daren. Welcome to my GitHub profile!

             

Background

Ph.D., Quantitative Biology (Evolutionary Biology, Genetics, Genomics, & Bioinformatics) from University of Texas, Arlington.

Main academic interest: Convergent, adaptive evolution of vertebrates using cutting-edge genomics approaches.

Currently a postdoctoral fellow in the Edwards lab at Harvard University.

Previously a graduate student studying in the Castoe lab at UT-Arlington.

Genomic Analysis Toolkit

Genome Sequencing, Assembly, & Annotation, RAD-seq, RNA-seq, ATAC-seq, Hi-C, and more!

Coding Languages

         

Badge Sources: Awesome Badges - https://github.com/Envoy-VC/awesome-badges and custom badges constructed using https://shields.io/

darencard.github.io's Issues

Repeat Annotation Blog

Hi Daren
Thanks for the great blogs you are making available.
I have spotted two errors in your https://darencard.net/blog/2022-07-09-genome-repeat-annotation/

1. -a should point to the known database in the following command (your original is given here):
   repclassifier -t 3 -d Tetrapoda -u reference-genome-families.prefix.fa.unknown
   -k reference-genome-families.prefix.fa.known -a reference-genome-families.prefix.fa.unknown
   -o round-1_RepbaseTetrapoda-Self

2. This command fails, with "datamash: invalid input: field 4 requested, line 1 has only 3 fields":
   cat 05_full_out/reference-genome.full_mask.out | tail -n +4 | awk -v OFS="\t" '{ print $6, $7, $11 }' |
   awk -F '[\t/]' -v OFS="\t" '{ if (NF == 3) print $3, "NA", $2 - $1 +1; else print $3, $4, $2 - $1 +1 }' |
   datamash -sg 1,2,3 sum 4 | grep -v "?" |
   awk -v OFS="\t" -v genomeLen="${allLen}" '{ print $0, $4 / genomeLen }' > 05_full_out/reference-genome.full_mask.tabulate

Best, Ovidiu

question of your blog named "Tutorial for running OrthoMCL"

Hi,
When I read your blog named "Tutorial for running OrthoMCL" at http://darencard.net/blog/2018-01-12-orthomcl-tutorial/, I can not understand the meanning of your sentence below.
Let’s say we have our protein FASTA files (i.e., _protein.faa) and our annotation data (stored with a _protein_table.txt suffix) stored in a directory called raw in our working directory.
Where are your annotation data such as GCF_000090745.1_AnoCar2.0_protein_table.txt from? Is it from ncbi ? I can not find the annotation data of protein.
I would appreciate it if you would give me a reply.
Thanks,
sunxh,