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1 Ergebnisse
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Software to support titled: Self-cleaving guide RNAs enable..:
Pelz, Carl
;
Tiyaboonchai, Amita
;
Grompe, Markus
doi:10.5281/zenodo.7268403. , 2022
Link:
https://zenodo.org/record/7268404
RT Journal T1
Software to support titled: Self-cleaving guide RNAs enable pharmacological selection of precise gene editing events in vivo
UL https://suche.suub.uni-bremen.de/peid=base-ftzenodo:oai:zenodo.org:7268404&Exemplar=1&LAN=DE A1 Pelz, Carl A1 Tiyaboonchai, Amita A1 Grompe, Markus YR 2022 K1 For the custom alignments K1 Bowtie version 1 was used to create custom indexes and align data from knock in mouse model. Indexes were made from selected knock in sequence and transcripts of targeted genes. Default parameters were used to build indexes. A 50 base wide window (shifted in steps of 15 bases) was used to go through the sequenced data looking for alignments and selected the first valid alignment found. For valid alignments K1 3 mismatches were allowed K1 but required unique best matches (--best --strata -v 3 –m 1). Once all alignments were found K1 full sequences were stacked based on positions of windowed alignment. This allowed us to see the "overhang" (in an unbiased way) where our knock in sequence was inserted into the host genome (mouse genome assembly GRCm38). Paired end sequencing was performed K1 but aligned to pair ends independently. The alignment strategy did not generate many mated pairs and mated pairs were not required K1 but when counting alignments K1 mated pairs were only counted once JF doi:10.5281/zenodo.7268403 LK http://dx.doi.org/https://zenodo.org/record/7268404 DO https://zenodo.org/record/7268404 SF ELIB - SuUB Bremen
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