Hi,
I am trying to run tophat with R1 and R2 Illumina unpaired reads (R1:20mil and R2:10 mil). I need to run it against different small viral reference genome but I am having trouble assembling i with tophat even if I now that the reference is in. I've tried to set the flag for allow more mismatches so I used:
>> tophat --library-type fr-unstranded --allow-partial-mapping reference_seq --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 R1,R2
Am I making mistakes with the setting? can I allow more than 3 mismatches or use R1 and R2 in a different way???
Any help or advice will be great.. also suggestion for other program
Thanks
F.
I am trying to run tophat with R1 and R2 Illumina unpaired reads (R1:20mil and R2:10 mil). I need to run it against different small viral reference genome but I am having trouble assembling i with tophat even if I now that the reference is in. I've tried to set the flag for allow more mismatches so I used:
>> tophat --library-type fr-unstranded --allow-partial-mapping reference_seq --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 R1,R2
Am I making mistakes with the setting? can I allow more than 3 mismatches or use R1 and R2 in a different way???
Any help or advice will be great.. also suggestion for other program
Thanks
F.
