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RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter #696

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grennfp opened this issue Oct 5, 2023 · 1 comment
Open

RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter #696

grennfp opened this issue Oct 5, 2023 · 1 comment

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@grennfp
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grennfp commented Oct 5, 2023

Running alignment with the STAR wasp option creates *toTranscriptome.out_wasp_qc.bam files. When running RSEM, the code expect the files to not include "_wasp_qc" in the name, causing an error.
@gaow
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gaow commented Feb 26, 2024

@grennfp is this fixed now? It looks like a file naming issue that can be addressed with a bit of SoS/python syntax?

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@gaow @grennfp