bwa mem -t $Ncpu -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3 ../humangenomes/hg38.fa $filename.R1.fastq.gz $filename.R2.fastq.gz | samtools view -Sbh > $filename.bam

Can I use above bam file for feature counts, how will it handle chimeric alignment and what is the quality for linear match with the above parameters. Is there any away I can filter bam file from above command to pass it to feature count. This is what I use right now.

featureCounts -p -T 5 -a hg38GENCODE.gtf -o $filename.txt $filename.bam &

I am running data in bulk, that requires bwa mem with above parameters so do not want to use resources for e.g. STAR alignment etc for passing it to featureCount.

I am very new to this field, so please direct me to good literature for all these things. I am still understanding bwa mem algo and how these parameters will affect the results.

I'm pretty sure bwa-mem is not splice aware, so it's not suitable for RNASeq. You really should use STAR.