featurecounts

conda search subread
conda install subread

featureCounts 
-a gtf  # Name of an annotation file. GTF/GFF format by default.
-o outputfile # Name of output file including read counts
-t exon/gene  # Specify feature type(s) in a GTF annotation . 'exon' by default.
-f    # Perform read counting at feature level (eg. counting reads for exons rather than genes).
-O # Assign reads to all their overlapping meta-features (or features if -f is specified).
-M # Multi-mapping reads will also be counted.
--minOverlap <int>  # Minimum number of overlapping bases in a read that is required for read assignment. 1 by default.
-p # If specified, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads
-B # Only count read pairs that have both ends aligned.
-P # Check validity of paired-end distance when counting read pairs. Use -d and -D to set thresholds.
-d <int>   # Minimum fragment/template length, 50 by default.
-D <int>   # Maximum fragment/template length, 600 by default.
-C      # Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.
-T <int>  # Number of the threads. 1 by default.

featureCounts -a ~/software/STAR-2.7.7a/genome_gtf/gencode.vM29.annotation.gtf -o all_sample -t exon -T 10  SRR679*.sort