Hello all, I'm new to SeqAnswers and I'm excited to contribute to the community. That being said, I was wondering if anyone has some tips for me. My goal is to learn how to simulate reads (such as from an Illumina) from a fasta file with a human reference chromosome information. This is what I have: the downloaded fasta files, SAMtools (haven't used them before though), WGSim (also have never used), and R. I have been trying to follow this tutorial http://biobits.org/samtools_primer.html but I seem to be stuck. First off, if I've downloaded Samtools do I need to 'build' it? I'm not sure what that means or where I enter the commands.I understand that once everything is in place this would be my first step, entering---> wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>. I assume I replace 'ref' from <in.ref.fa> with the filename for the reference chromosome (please correct me if I'm wrong). However, I can't figure out where to enter this command either. When I open WGSim it lists a long piece of code that I do not understand, and I don't see any command line. Any guidance would be greatly appreciated!
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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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