Aligning multiple paired-end samples tophat2 command line

Question

[nash.claire]

Hi all,

Really sorry for the seemingly basic and stupid question. I'm a beginner to unix and the command line and just want to clarify.

If I want to run multiple paired-end samples with tophat2 from the command line (I have 30 samples and a Mac pro with 12 cores and 64gb RAM), how exactly should the command be written? The tophat manual wasn't that clear to me for this and all the tutorials out there don't really specify how to run multiple samples. Would it be like this......

tophat2 -o /path/to/directory -p 12 /path/to/indexes/hg19 read1_1.fq, read2_1.fq, read3_fq, read1_2.fq, read2_2.fq, read3_2.fq

Where do the brackets and commas go if they are needed?

[nash.claire]

Thank you so much Antonio that's great! I will try it out

[nash.claire]

Hi

I tried the command you detailed and it wouldn't work. It keeps saying that for my second sample, there is no such file or directory. I think I've read somewhere that this can be a memory/processor issue? I have checked and the file name and path are correct (no typing errors). Unless it's something with the command??

Answer 1

[Antonio R. Franco]

You can define in options a lot more things, like the type of library (--library-type), the inner size of your reads, the standard deviation..

But I see you are confuse with the way of indicating the fastq files. If I am not wrong...

If you have only a couple of paired end sequences you separate both files with a empty space

tophat options <index file> file_1.fastq file_2.fastq
___________place a space here___________^

If you have more than one couple of paired end fastq files, you define with the colon the first reads in first place, then a empty space, and then the mate reads separated again by a colon

tophat options <index file> file_1.fastq,another_file_1.fastq,yet_another_file1.fastq file_2.fastq,another_file_2.fastq,yet_another_file2.fastq
________________________________________________________place a space here___________^