News
News & blog posts
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Processing rMATS output
May 25, 2023
rMATS outputs several files, including txt files for all considered splicing events (i.e. SE (skipped exon), MXE (mutually exclusive exons),...
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Alternative splicing and Snakemake
May 18, 2023
In this and next few posts, I will log my attempt to replace shell scripting (which I have been using...
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The lab has grown!
December 20, 2022
In the autumn of 2022 we have welcomed two new lab members. Bogna joined as a lab manager and Ola...
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TT-seq analysis -Spliced reads
December 20, 2022
In this post, I will continue with reproducing the analysis from Shao et al and compare spliced reads across...
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TT-seq analysis - Metagene profiles 2
September 22, 2022
In this post, I will re-plot the graphs created using ngsplot, to combine the sense and anti-sense profiles on a...
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TT-seq analysis - Metagene profiles
September 15, 2022
In this post, I will use ngs.plot to visualize the results of TT-seq experiment around functional genomic regions, i.e. transcription...
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TT-seq analysis - TU annotation
August 18, 2022
In this post, we will use R shiny application developed by Shao et al. (1), to annotate transcriptional units in...
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New lab space
August 17, 2022
We moved to the Centre of Advanced Technologies. It is not far - geographically speaking, but it is a big...
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TT-seq analysis - BigWig files
July 07, 2022
In this post, we will use previously calculated scale factors to create scale and strand-specific BigWig files. These files can...
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TT-seq analysis - Scale factors
June 23, 2022
In this post, I will normalize the sequencing samples, using the read counts from ERCC spike-ins. To this end I...
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TT-seq analysis - Step 1
June 16, 2022
The data I have been working with are the result of TT-seq experiment performed by Shao et al., who set...
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Reads alignment
May 26, 2022
Today, I will start the analysis of the data and align the pair-end reads to mm10 reference sequence using STAR.
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Downloading fastq files.
May 19, 2022
Let’s pick it up where we left it last time. SRA explorer provides as with basic bash script that we...
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Accessing and downloading raw sequencing data.
April 21, 2022
GEO does not store raw data. As confusing as it seems, GEO does not store raw sequence data. Various formats...
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Downloading data from GEO to HPC.
April 14, 2022
Most, if not all (published) NGS data is deposited to GEO repository and available to download and process. Today the...
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Bash profile
April 07, 2022
We will be using shell to do most of our work. Shell accepts and runs commands. When you login, few...
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Welcome to Maslon Lab
March 24, 2022
Welcome to our website. This space will be used to advertise new positions, talk about our research and share my...