Question: Confusion in Tophat2 input files
gravatar for Nitin Sharma
2.9 years ago by
Nitin Sharma30
Institute for Cancer Research, Dept. of Tumor Biology, Oslo University Hospital, Oslo, Norway
Nitin Sharma30 wrote:

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]&gt; [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


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


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


Something else

If I can use more than option than what is difference between them

Thanks in advance

rna-seq alignment tophat • 854 views
ADD COMMENTlink modified 2.9 years ago by WouterDeCoster40k • written 2.9 years ago by Nitin Sharma30

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

ADD REPLYlink written 2.9 years ago by Angel3.5k
gravatar for WouterDeCoster
2.9 years ago by
WouterDeCoster40k wrote:

Alignment is performed per sample, i.e. the command is ran for each sample separately. So that would be option 1.

ADD COMMENTlink written 2.9 years ago by WouterDeCoster40k
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