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Scallop2 always runs --preview? #5

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OXB-DC opened this issue Jul 7, 2022 · 0 comments
Open

Scallop2 always runs --preview? #5

OXB-DC opened this issue Jul 7, 2022 · 0 comments

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@OXB-DC
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OXB-DC commented Jul 7, 2022

Hi and thanks for developing Scallop2!

I was just trying it out and noticed that when running Scallop2 it always seems to attempt to preview the strandness irrespective of whether I want it to or not. This is an issue for me as due to the nature of my reads it is unable to infer strandness (even though I am sure it is "first" [dUTP method] - I believe this may be related to the fact that ~99% of my reads originate from the top strand of my custom genome as there is no transcriptional activity from the bottom strand).

This means that I always get the error message shown below:

command line: scallop2 -i <snip>.bam -o <snip>.gtf --verbose 2 --min_mapping_quality 1 --library-type first 

preview strandness: sampled reads = 2000000, single = 0, paired = 2000000, first = 19232, second = 0, inferred = unstranded, given = empty
not enough paired-end reads to create the profile (0 collected)

And consequently Scallop2 never runs fully. It works fine with Scallop(1) so there must be difference in the code here. Can you make the inference of strandness optional please?

@OXB-DC OXB-DC changed the title Scallop2 always run --preview? Scallop2 always runs --preview? Jul 7, 2022
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