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The reason for this changing is to keep alignment with the structure of the MSE transfer chart for BP-based iterative channel decoding and state estimation.
These were also surrounded with packs of sausages and re-placed on the motion table as in a patient acquisition procedure, with no attempt to keep alignment orthogonal by any other means than manual placement.
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Perform local alignment between the genome and each read individually, and keep alignments that have score higher than a threshold.
In practice we used two sets of alignment filters and kept alignments that passed one or both sets.
To keep the alignment of SiC NFs, the optimized spinning time is 5 min.
If a read is mapped to the genome uniquely, we keep its alignment without additional requirements.
Keep this alignment to reduce pain spikes.
Make sure to keep the alignment pin in its hole as you put the new pump in place.
We note that by doing so we allow the reads to unbiasedly align to their best locations in the splice-junction aware genome and subsequently keep our alignments of interest as opposed to aligning the read data directly to the transcriptome (e.g., Roberts and Pachter, 2013).
Limiting read alignment to affected regions of the assembly Since only a small portion of the assembly is affected in each step, we can keep most alignments from the previous iterations and only align reads to the regions that changed.
Between consecutive iterations, we keep all alignments for each sequence window of the assembly and recompute only alignments to affected windows, as outlined above.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com