dear all,
This might be very silly question but i hope you can help to clear my doubts
from TopHat mannual
tophat [options]* <genome_index_base> <reads1_1[,...,readsn_1]> [reads1_2,...readsn_2]<="" p="">
Now, if i have a control and treated biological triplicate samples as paired-end reads what will be the right command
1) tophat [options]* <genome_index_base> control1_1 control1_2 tophat [options]* <genome_index_base> control2_1 control2_2 tophat [options]* <genome_index_base> control3_1 control3_2
tophat [options]* <genome_index_base> Treated1_1 Treated1_2
tophat [options]* <genome_index_base> Treated2_1 Treated2_2
tophat [options]* <genome_index_base> Treated3_1 Treated3_2
OR
2) tophat [options]* <genome_index_base> control1_1,control2_1,control3_1 control1_2,control2_2,control3_2 tophat [options]* <genome_index_base> Treated1_1,Treated2_1,Treated3_1 Treated1_2,Treated2_2,Treated3_2
OR
3) tophat [options]* <genome_index_base> control1_1,control2_1,control3_1,Treated1_1,Treated2_1,Treated3_1 control1_2,control2_2,control3_2,Treated1_2,Treated2_2,Treated3_2
OR
Something else
If I can use more than option than what is difference between them
Thanks in advance
•
written
by
CuriusScientist
1 answer
Alignment is performed per sample, i.e. the command is ran for each sample separately. So that would be option 1.
Log in to answer this question.
I think you should run tophat for each sample separately to produce a bam file for each sample. I mean for example you should run tophat on control1-1 and control1-2 (paired-end) once then control 2-1, control 2-2, etc independently