Question: why tophat2 saying that --max--deletion-length not recognized???
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5.0 years ago by
A3.9k wrote:

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??



myposts tophat2 bowtie2 • 1.1k views
ADD COMMENTlink written 5.0 years ago by A3.9k

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. 

ADD REPLYlink written 5.0 years ago by Ashutosh Pandey12k

yes exactly

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

thank you

ADD REPLYlink modified 10 months ago by RamRS30k • written 5.0 years ago by A3.9k
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