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Choose whether alignment and/or pseudoalignment are run #77

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Nick-Eagles opened this issue Sep 27, 2021 · 0 comments
Open

Choose whether alignment and/or pseudoalignment are run #77

Nick-Eagles opened this issue Sep 27, 2021 · 0 comments
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@Nick-Eagles
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enhancement New feature or request
Milestone
bioc v3.22

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@Nick-Eagles
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Currently, SPEAQeasy always aligns inputs to a reference genome and pseudo-aligns to a reference transcriptome. In theory, a user might only want to do one or the other. Consider a command-line option --align_mode [option], where [option] might be "genome", "transcriptome", or "both" (where "both" is the default).
@Nick-Eagles Nick-Eagles self-assigned this Sep 27, 2021
@lcolladotor lcolladotor added the enhancement New feature or request label Nov 30, 2023
@lcolladotor lcolladotor moved this to Todo in SPEAQeasy plans Nov 30, 2023
@lcolladotor lcolladotor added this to the bioc v3.22 milestone Nov 30, 2023
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@Nick-Eagles Nick-Eagles

Labels
enhancement New feature or request
Projects
SPEAQeasy plans
Status: Todo
Milestone
bioc v3.22
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@lcolladotor @Nick-Eagles