why tophat2 saying that --max--deletion-length not recognized???
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?
1 answer
--max--deletion-lengthshould be--max-deletion-length. Observe your errors closely before posting them :-)- Ignore the warning. You can't do much about it.
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Ashutosh Pandey
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