MartGro

## How to align long sequences with BWA
Aligning > 1MB long sequences (e.g. long DNA sequences) can take quite long with Needleman Wunsch

An alternative is using the BWA:
http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf

#1 Create index:
../bwa-0.7.17/bwa index -p index_path -a bwtsw dna_reference.fasta


./bwa-0.7.17/bwa mem -t 16 index_path dna_of_interest.fasta | ./samtools-1.16.1/samtools sort -o output.bam -

## napari_image_display_widget.py
import sys
from PyQt5.QtWidgets import QApplication, QLabel
from PyQt5.QtGui import QPixmap

class ImageWidget(QLabel):
    """
    A QLabel widget that displays an image from a file
    """
    def __init__(self, parent=None):
        """

## RSP1_instructions.md

      
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                Getting the RSP1 to run under Ubuntu 20.04
              
          
Get the Driver

Download the driver from the following link:
https://www.sdrplay.com/dlfinishs/

Follow the Instructions of CubicSDR

For instructions on how to build CubicSDR on Linux, refer to the following link:

  
## conda_dependencies.txt
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=main
_openmp_mutex=5.1=1_gnu
argcomplete=3.1.1=pypi_0
argh=0.27.2=pypi_0
biopython=1.79=pypi_0
ca-certificates=2023.7.22=hbcca054_0
certifi=2016.9.26=py36_0

## IQ Samples
Places where you can find recordings of radio signals with different modulations:

https://www.sdrangel.org/iq-files/
https://www.sdrplay.com/iq-demo-files/
https://lucasteske.dev/satcom-projects/sample-baseband-files

## installing rmats
https://bioconda.github.io/recipes/rmats/README.html

1) install it via conda
conda install rmats -c bioconda

2) check
which rmats.py
	Aligning > 1MB long sequences (e.g. long DNA sequences) can take quite long with Needleman Wunsch

	An alternative is using the BWA:
	http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf

	#1 Create index:
	../bwa-0.7.17/bwa index -p index_path -a bwtsw dna_reference.fasta


	./bwa-0.7.17/bwa mem -t 16 index_path dna_of_interest.fasta \| ./samtools-1.16.1/samtools sort -o output.bam -
	import sys
	from PyQt5.QtWidgets import QApplication, QLabel
	from PyQt5.QtGui import QPixmap

	class ImageWidget(QLabel):
	"""
	A QLabel widget that displays an image from a file
	"""
	def __init__(self, parent=None):
	"""
	# This file may be used to create an environment using:
	# $ conda create --name <env> --file <this file>
	# platform: linux-64
	_libgcc_mutex=0.1=main
	_openmp_mutex=5.1=1_gnu
	argcomplete=3.1.1=pypi_0
	argh=0.27.2=pypi_0
	biopython=1.79=pypi_0
	ca-certificates=2023.7.22=hbcca054_0
	certifi=2016.9.26=py36_0
	Places where you can find recordings of radio signals with different modulations:

	https://www.sdrangel.org/iq-files/
	https://www.sdrplay.com/iq-demo-files/
	https://lucasteske.dev/satcom-projects/sample-baseband-files
	https://bioconda.github.io/recipes/rmats/README.html

	1) install it via conda
	conda install rmats -c bioconda

	2) check
	which rmats.py