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Add alignment #14

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pinin4fjords opened this issue Feb 19, 2024 · 1 comment · Fixed by #12
Closed

Add alignment #14

pinin4fjords opened this issue Feb 19, 2024 · 1 comment · Fixed by #12
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enhancement New feature or request
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v1.0.0

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Description of feature

We need both transcriptome and genome alignment for use by different modules associated with Riboseq. This can be adapted from what nf-core/riboseq does.
@pinin4fjords pinin4fjords added the enhancement New feature or request label Feb 19, 2024
@pinin4fjords pinin4fjords linked a pull request Feb 19, 2024 that will close this issue
Add alignment via STAR + postprocessing #12
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@pinin4fjords
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We ended up implementing this using fastq_align_star (subworkflow) from nf-core/modules. What nf-core/rnaseq does is a bit messy and complicated by igenomes usage which is not currently very helpful for RNA-studies.

I ended up doing a bit of work alongside to fix up that module for better transcriptome alignment handling: nf-core/modules#4927.

@pinin4fjords pinin4fjords added this to the v1.0.0 milestone Feb 19, 2024
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enhancement New feature or request
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Add alignment via STAR + postprocessing nf-core/riboseq
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