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After preprocessing analyses, we mapped the remaining sequences to the reference pepper genome (Data Citation 1: figshare https://doi.org/10.6084/m9.figshare.org/10.6084/m9.figshare
We succeeded for 20 LGs, and mapped the remaining eight separately because they lacked sufficient anchoring markers.
We mapped the remaining domains onto the set of proteins in P. Rosetta stone proteins are those that have two or more fused domains encoded by a single gene in one species, but whose constituent domains are encoded by separate genes as single domain proteins in the same or another species [22].
After the removal of larger RNAs, we mapped the remaining reads (18 30 nt) to miRBase 16.0 [ 31] using the deep-sequencing small RNA analysis pipeline (DSAP).
To classify reads that did not map to miRNAs in miRBase, we mapped the remaining reads to multiple databases in order to distinguish alternative read sources.
We then mapped the remaining reads to the Cassava genome (or castor bean genome) using Bowtie [ 59] and merged neighboring loci if they shared overlapping reads.
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In the second phase, we map the remaining nodes if possible and calculate final alignment score.
For AS-30CQ, the final 9 base calls were universally of poor quality and were removed before mapping the remaining 41 base sequence strings.
After mapping the remaining reads to the genome, we employed a second sequence redundancy reduction step for the analyses investigating the overlap between our reads and genomic features such as ENCODE regions, ncRNAs or genes.
Then, tags originating from rRNAs, tRNAs, snRNAs, and snoRNAs were removed by mapping the remained sRNA tags to the ncRNA annotation database of T. urticae (https://bioinformatics.psb.ugent.be/gdb/tetranychus/small_RNAs/).psb.ugent.be/gdb/tetranychus/small_RNAs/
Three genes (AaHsp70Bb, AaHsp70Bb' and AaHsp70Ca') had no reads mapping in any sample, whereas <10 reads mapped to the remaining genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com