Sequence analysis
Sequence files were retrieved from the MiSeq illumina platform as a raw
FASTQ file. Sequences corresponding to the coding regions were extracted
using a pattern search program written by Perl script. Only the
sequences with an 8 nucleotide perfect match upstream of the start codon
and downstream of the random region are considered as reliable for
downstream analysis. The reliable sequences (in FASTQ format) were
further processed using FASTAptamer-count (Alam, Chang, & Burke, 2015)
to rank sort sequences based on their read counts. Consensus sequence
logos were created using WebLogo 3 (Crooks, Hon, Chandonia, & Brenner,
2004) based on the top 50 reads with specific conditions (fixed letter
and positions).