Changes in version 1.34.0 o New functions: simReads() and scanFasta(). simReads() generates simulation RNA-seq reads for transcripts. o align() and subjunc() estimate fragment length from mapped read pairs and use the estimated length to assist reporting the best alignment. o align() and subjunc() prefer alignments with no indels included over indel-containing alignments when same number of matched bases are found. o align() and subjunc() check if index files were successfully loaded before starting read mapping. o align() and subjunc() detect indels arising from incorrect shifting of seed sequence when being mapped to low-complexity region and exclude such indels from read re-alignment and indel reporting. o buildindex(), align() and subjunc() support gzipped FASTA format. o featureCounts() allows mapped reads to have ‘*’ as their chromosome name. o removeDupReads() supports BAM-format input and output. Changes in version 1.32.0 o New function flattenGTF() that merges overlapping features into a single interval. o New parameter for align() and subjunc(): sortReadsByCoordinates. o New parameters for featureCounts(): readShiftType, readShiftSize and additionalAttributes. o Specify strand protocol for each library individually in featureCounts(). o Much improved speed of align() and subjunc(). o align() and subjunc() return mapping statistics. o Default setting of buildindex() is changed to building a one-block full index.