Cufflinks hidata1/9/2024 fastq example is as follows: Jyothi Thimmapuram, Ph.D. This format preserves the most sequencing information as possible, including quality scores for each sequenced base. STEP 1: PREPARING THE DATA The raw data obtained from a sequencing center will typically be minimally processed and in the. Use the following command to download a copy of this guide. cd DataĪnother method of moving/obtaining data is by downloading weblinks through UNIX. Now that the files have been downloaded and expanded, enter the same directory as the data. The file is a compressed package containing all necessary files for the workshop. Make a new directory in your scratch space, navigate into that directory, and download the workshop data pack. Bioinformatics Core DirectorĭOWNLOADING MATERIALS After logging into the cluster, the current working directory will be /home/username. Limited access, free Hansen cluster accounts are provided upon request – contact Today’s Hansen access is temporary and meant for use with this workshop only If using OSX, open terminal and enter: ssh PuTTY is a free program available for Windows. GETTING STARTED Login to the Hansen cluster using the provided credentials and PuTTY: The analysis will be limited to the short mouse chromosome 19 to ensure completion in a timely manner. This workshop will determine the differential gene expression (DGE) between two treatments, early neurogenesis sample t7 and maturing glutamatergic neuron sample t21, with three replicates for each treatment. One such study, SRA ID# SRP017778, investigates the transcriptional changes of mouse murine embryonic stem cells as they differentiate into glutamatergic cortical neurons. Additionally, each participant needs to have a temporary computing account to access the Hansen cluster, which will be provided upon registration.ĮXPERIMENTAL DESIGN The Sequence Read Archive (SRA) is a database hosted by NCBI that provides a means for researchers to deposit their primary sequencing data for published studies. Without having a working knowledge of UNIX, it will be very difficult to perform the tasks necessary to conduct the analysis, and teaching such UNIX skills is beyond the scope of this particular workshop. Bioinformatics Core RNA-SEQ WORKSHOP, APRIL 2015 – PREREQUISITES This workshop assumes the user is comfortable operating in the UNIX environment.
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