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While smooth retinotopy is constraining, studies suggest that it improves both wiring economy and the V1 population code read downstream.
Because HMMSplicer must match the second piece of the read downstream of the initial exon edge identified, the HMMSplicer algorithm is sensitive to maximum intron size.
SpliceMap divides reads in half, aligns each read half to the genome, then locates the remaining part of the read downstream within the maximum intron size.
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DESeq results were consistent with a 3′-UTR extension, showing an approximately 10-fold increase (padj =5.29E-06) of reads downstream of PCL5 in the tfc6 mutant strains.
A well-positioned nucleosome typically exhibits the enrichment profile shown in Figure 1: a peak of positive strand reads upstream of the nucleosome location, and one of negative strand reads downstream.
The full-length sequence is then used in place of the read in downstream analysis.
Reads were combined into unique reads by collapsing all identical reads to one read for downstream analysis.
These criteria retained only the perfectly matched reads for downstream analysis.
Numbers of filtered RNA-Seq reads for downstream analyses.
Any conclusions drawn from such reads in downstream analyses will be unreliable.
Any conclusions drawn in the presence of uniquely misaligned reads in downstream analyses will be unreliable.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com