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locarna alignments ohne constraints #1

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martin-raden opened this issue Jul 1, 2024 · 6 comments

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martin-raden commented Jul 1, 2024 •

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ausgeschnittenen seqs 3' und 5'
(a) keine constraints (zyklisierungsmodell mit eingeschränktem 3'SL und allen interaction sites)
(b) keine long range base pairs als constraint (lineares modell mit vollem 3'SL)
ergebnis-ZIPs ins repo downloaden...

martin-raden self-assigned this

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martin-raden commented Jul 15, 2024

locarna-p @ 18°C - unconstraint (nur linker und AUG anchor)

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martin-raden commented Jul 15, 2024

locarna-p @ 18°C - unonstraint - nur 3' teil

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martin-raden commented Jul 15, 2024 •

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5' komplette UTR mitnehmen, um lokale strukturen zu erhalten (check MBFV effekt) - Data/parameter_table.csv
@mtw : mehr TBFV sequences

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martin-raden commented Jul 15, 2024 •

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locarna call mit cofold-structure constraints (analog zu intarna pipeline)

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martin-raden commented Jul 15, 2024 •

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vergleich interaction pattern 18 vs 37 °C ... irgendwelche unterschiede? ggf. bei 37 °C mehr interaction?

KEIN NENNENSWERTER EFFEKT BEI MBFV ... DAHER ALS EGAL VERBUCHT

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martin-raden commented Jul 15, 2024

script für lokalen locarna call...

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