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I have no output for mop_preprocess in the files : alignement, counts, cram_files (the files are empty). #45

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matjack2000 opened this issue Apr 27, 2023 · 4 comments
Open

I have no output for mop_preprocess in the files : alignement, counts, cram_files (the files are empty). #45

matjack2000 opened this issue Apr 27, 2023 · 4 comments

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@matjack2000
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I'm pretty sure this is due to the fact that the alignment with minimap2 is not working and that this may be caused by my data.
final_summary_FAW56164_db7c5011_600df0f2no_depletion.txt
maturemini.fa.gz
params.config.zip
@lucacozzuto
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Can you show the log?

@matjack2000
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log8.zip

@lucacozzuto
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Hi is your reference a genome or transcriptome? if with small RNA I think minimap / graphmap is not really a good idea, I fear. You could try bwa (it is supported)

@matjack2000
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I use the transcriptome, ok I will try with bwa thanks.

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@lucacozzuto @matjack2000