@shortlongseq
Your friendly bioinformatician.
I'm writing this blog to help biologists, or aspiring computational biologist/ bioinformaticians, with little to no experience in coding. Hopefully my writing can help some people who are trying to use computational methods to analyze biological data.
Medium: https://shortlongseq.medium.com/
Substack: https://seqbioinformatics.substack.com/
BuyMeACoffee: https://www.buymeacoffee.com/shortlongseq
Nothing here yet.
Oct 6, 2023 · 3 min read · We learned how to quality control, align sequences and generate DEG analysis using the cufflink tool. What if I want to create just a count matrix? In this write-up, I'm going to show you how to make a count matrix. Image credit: Lafzi et al. Tutoria...
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Sep 8, 2023 · 6 min read · Variant Calling is used when one wants to identify differences in genomic sequence such as SNP (single nucleotide polymorphism), insertions, deletions and structural variations between samples, or subjects of interest, and a reference genome (or tran...
Join discussionMar 6, 2023 · 11 min read · In this article, I will walk you through how to conduct a de novo transcriptome analysis. If you remember from my previous article, de novo analysis is used when there is no genome reference to map the sequence reads against. Therefore you will need ...
Join discussionJan 16, 2023 · 7 min read · Preliminary Preparation: Before we start, there are a couple of tools (hyperlinked) to download: HISAT2, Cufflinks, Samtools, and Bowtie2. Make sure you have the correct binary and the latest version when downloading and follow the instructions to in...
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Dec 30, 2022 · 2 min read · Continuing in our series, the next part I will be discussing is sequence mapping. Referring back to this diagram below after cleaning (quality control) the sequence data we have to align the sequence reads. What does aligning mean? It means "arrangi...
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