why tophat2 saying that --max--deletion-length not recognized???

Question

[zizigolu]

Hi friends,

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?

Answer 1

[Ashutosh Pandey]

1. --max--deletion-length should be --max-deletion-length. Observe your errors closely before posting them :-)
2. Ignore the warning. You can't do much about it.

[zizigolu]

yes exactly

you all right about the --max-deletion-length

thank you