cmdcolin

src/App.tsx(21,24): error TS2339: Property 'showTrack' does not exist on type 'IModelType<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; displayName: IMaybe<ISimpleType<string>>; minimized: IType<boolean | undefined, boolean, boolean>; } & { id: IOptionalIType<ISimpleType<string>, [undefined]>; type: ISimpleType<"LinearGenomeView">; offsetPx: IType<number | undefined, number, number>; bpPerPx: IType<number | undefined, number, number>; displayedRegions: IOptionalIType<IType<Region[], Region[], Region[]>, [undefined]>; tracks: IArrayType<IAnyType>; hideHeader: IType<boolean | undefined, boolean, boolean>; hideHeaderOverview: IType<boolean | undefined, boolean, boolean>; hideNoTracksActive: IType<boolean | undefined, boolean, boolean>; trackSelectorType: IOptionalIType<ISimpleType<string>, [undefined]>; showCenterLine: IOptionalIType<ISimpleType<boolean>, [undefined]>; showCytobandsSetting: IOptionalIType<ISimpleType<boolean>, [undefined]>; trackLabels: IOptionalIType<ISimpleType<string>, [undefined]>

cmdcolin

cmdcolin

$ git clone https://github.com/goodarzilab/lorna-sh
$ cd lorna-sh

## look around...i decided to try starting in processing_seqs
$ find .
$ cd processing_seqs

## in R repl, install dependencies 
## data.table
## optparse

cmdcolin

What does RNA-seq look like in the genome browser?

here is a picture of a "RNA-seq BAM file" in JBrowse 2

(live link https://jbrowse.org/code/jb2/v2.16.1/?config=test_data%2Fconfig_demo.json&session=share-i3nrunRxkg&password=S1tAc)

you can see that there are all these little grey boxes and the black lines connecting them. These are the so-called "reads" in the RNA-seq BAM file! there is also a little "histogram" along the top. This is showing how many "reads" mapped to a given position in the genome

cmdcolin

## step 1, get miniconda
./Miniconda3-latest-Linux-x86_64.sh # follow a bunch of y/n questions in here

## for me, i did not activate it by default so i manually activate it like this in zsh shell
eval "$(/home/cdiesh/miniconda3/bin/conda shell.zsh hook)"  


## then activate environment
conda create -n tf2_10 python=3.9
conda activate tf2_10

cmdcolin

~/Downloads ❯❯❯ eval "$(/home/cdiesh/miniconda3/bin/conda shell.zsh hook)"

(base) ~/Downloads ❯❯❯ conda activate tf2_10                                                     ✘ 1
(tf2_10) ~/Downloads ❯❯❯ python3 -m pip install tensorflow==2.10 numpy==1.24
Collecting tensorflow==2.10
  Using cached tensorflow-2.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB)
Collecting numpy==1.24
  Using cached numpy-1.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting absl-py>=1.0.0 (from tensorflow==2.10)

cmdcolin

~/Tiberius ❯❯❯ python3 -m venv  .venv                                                                                                                                                                 ✘ 130
~/Tiberius ❯❯❯ .venv/bin/activate
zsh: command not found: .venv/bin/activate
~/Tiberius ❯❯❯ source .venv/bin/activate                                                                                                                                                              ✘ 127
(.venv) ~/Tiberius ❯❯❯ pip install tensorflow_probability==0.18.0 transformers pyBigWig bio scikit-learn biopython bcbio-gff requests
Collecting tensorflow_probability==0.18.0
  Downloading tensorflow_probability-0.18.0-py2.py3-none-any.whl.metadata (13 kB)
Collecting transformers
  Downloading transformers-4.44.2-py3-none-any.whl.metadata (43 kB)
Collecting pyBigWig

cmdcolin

// usage:
// download this file to a file unprepare_seqs.js
// then run:
// node unprepare_seqs.js /path/to/seq/dir output_file.fa
// after that, fold the lines to a constant line length with:
// fold output_file.fa > output_file2.fa
const fs = require('fs')
const path = require('path')
const dir = process.argv[2] || '.'
const output = process.argv[3] || 'out.fa'

cmdcolin

#!/bin/bash
# gen_data.sh
# tags.txt is a list of git tags for a repo
cat tags.txt|while read p; do
  ## visit our specific JBrowse URL containing tag name in URL
  echo -n "$p"$'\t'; node get_page_size.js "https://jbrowse.org/code/jb2/$p/?config=test_data%2Fvolvox%2Fconfig.json&session=share-9NPMoB3dtz&password=aCI2W";
done;

cmdcolin

Tomasz Bednarczyk - I see you (Official Video) 2006 https://www.youtube.com/watch?v=lOx6fqT7Cys

 Emily Berregaard - A Poem [Strange Rules]  https://www.youtube.com/watch?v=liW_749IQ1U&
 
  Olympisk Løft - Tvillingeseglet (Full Album) [Janushoved]  2017 https://www.youtube.com/watch?v=-nMN7ZlUEj8
  
  angelo harmsworth and theodore cale schafer https://www.youtube.com/watch?v=60UiqNli2vs
  
  the yellow book https://www.youtube.com/watch?v=21S18AxFbjg