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Set chromap to not shift reads by default #381

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JoseEspinosa opened this issue Sep 27, 2024 · 0 comments
Open

Set chromap to not shift reads by default #381

JoseEspinosa opened this issue Sep 27, 2024 · 0 comments
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@JoseEspinosa
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enhancement New feature or request
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2.2

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Description of feature

The parameters used by chromap are the ones suggested for ATAC-seq in their documentation, see here. This includes the --Tn5-shift; thus, the shift is applied by default, unlike the rest of the aligners. As the --shift_reads parameter has been implemented now, it would make sense to not shift reads by default and only use the --Tn5-shift chromap parameter when the --shift_reads is set.
@JoseEspinosa JoseEspinosa added the enhancement New feature or request label Sep 27, 2024
@JoseEspinosa JoseEspinosa self-assigned this Sep 27, 2024
@JoseEspinosa JoseEspinosa added this to the 2.2 milestone Sep 27, 2024
@JoseEspinosa JoseEspinosa mentioned this issue Sep 27, 2024
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