Do I need combine two replicates?

[super0925]

Hi All, Just a quick question.
if I have two .fastq files are the same library but by running twice on the sequecing machine (they are not two unique samples). Do I need to combined them into one file to create first sample?
Thank you!

[dpryan]

Depends on what aligner (or other program) you'll be using. Some will allow you to use a list of files, others won't (in which case you'll need to just concatenate the files).

[super0925]

Depends on what aligner (or other program) you'll be using. Some will allow you to use a list of files, others won't (in which case you'll need to just concatenate the files).

Hi D
I am using Tophat2 , so do I need to combine two fastq file together and align it? or just select one of the file to do the mapping and downstream analysis?

[dpryan]

Tophat2 can accept a list of files, so just use that.

[super0925]

Tophat2 can accept a list of files, so just use that.

Sorry D, do you mean mapping two files at the same time or just select one of the replicates to do that?　 I think it is the former one, am I right?

[dpryan]

When you give tophat2 a list of files, it'll map them both and store the results in the same file. So yes, the former.

[super0925]

When you give tophat2 a list of files, it'll map them both and store the results in the same file. So yes, the former.

I have tried that, done!
Thank you so much!