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Old 01-14-2013, 06:40 AM   #1
alam
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Location: Waterloo

Join Date: Jan 2013
Posts: 1
Default Galaxy Tophat mapping problem: illumina paired end RNA data seq

Hi !
I am new in the forum. Having difficulties with the Tophat in Galaxy101. I am trying to map illumina paired end 50 bp sequences (77 million read )with Tetraodon genome by TopHat. After running several hours, I go following error message.

" 41: Tophat for Illumina on data 23 and data 22: accepted_hits
error
An error occurred running this job: TopHat v1.4.0 tophat -p 8 -r 20 -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --mate-std-dev 20 --i"

is there anybody to let me know what went wrong in the run?

Alam
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