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Update SSH key setup
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…submit when a GFF3 is present in both the 'reference' and 'star_reference' directory
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…b as outputs of stringtie
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… *ctab files required for input into ballgown)
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…nsfer individual log files to output
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…or GTF files
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Added support for single end reads. In the config file, the user must specify whether input datasets contain single or paired-end reads. A mixture of single and paired end reads cannot be used.
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…end reads as input
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…t files, a report of trimming and alignment statistics, QC_Report.tab, will be present in outputs directory
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Lowered default memory request and removed SRA ID as second input(takes hours to download the input data, user's may not want this for quick test runs)
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…e package to Compute nodes instead of using OASIS module
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…values
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Update README.md. Thanks Stephen!
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just a slight change to add a new line
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