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Two mismatches and an insertion at the most abundant position in the A. thaliana EST led to low counts for the FIP1 gene.
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Such extensions of numbers of targets will be feasible, as abundant positions are left for antigen spotting.
BMost abundant read position (of all tRNA reads).
The AAUAAA motif was also more abundant at position −21 in fungi (data not shown).
Similarly for ESP, the most abundant tag position was not counted because of a deletion in the A. thaliana ortholog.
A deletion in the Arabidopsis ESP gene at the most abundant tag position led to zero counts for ESP in the datasets with no mismatch allowed.
In summary, using a distant reference transcriptome resulted in a) fewer tags mapping, b) some genes not being surveyed for differential expression and c) lower than expected levels of expression for genes whose most abundant mapping position was not conserved.
To remove redundancy and maximize coverage, a single TSS was selected for each yeast ORF using a simple selection rule, taking the most abundant TSS position listed, or in the case of ambiguity, the longest UTR.
Type indicates whether gene is more or less abundant, or position and swapped amino acids (substitutions in bold are more likely to affect protein function than those in regular font).
For example, because the number of SNPs in the most abundant tag position of the ESM1 gene exceeded the number of mismatches allowed, expression levels for ESM1 were wrongly detected as being very low although the gene was still identified as differentially expressed in P. fastigiatum.
The distance between the two most abundant start positions as well as stop positions is 18 and 17 bases, which corresponds to the length of a primer, suggesting that in many cases primer sequences have not been trimmed from deposited sequences.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com