i typed the below syntax:
[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat2 --no-coverage-search --b2-sensitive --read-gap-length 12 --read-mismatches 2 --read-edit-dist 13 --max-insertion-length 20 --max--deletion-length 30 -p 8 -G genes.gtf genome SRR1944914_trimmed.fastq
tophat: option --max--deletion-length not recognized
do you know the reason please????
also a warning telling: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
what can i do??