General syntax question / feature request

[Marc Hoeppner]

Hi,

new user here, trying to familiarize myself with STAR. 

I have two things that sort of rubbed me the wrong way when trying to use star. As far as I can tell, there is:

- no built-in detection of compressed formats (only solved by adding a flag, which I guess is ok'ish but requires extra work for the user)

- no way to specify the output, either as file OR folder. 

This second point is really a major problem for me, since trying to model that behaviour (creating a folder, moving into the folder and executing the mapping) is majorly cumbersome  in a pipeline framework where I may want to process 20 samples in parallel. Tophat solves this by using the -o flag. Are there any thoughts to add this option perhaps?

Kind regards,

Marc

[Kirill Tsyganov]

Hi Marc, 

If you supplying your FASTQ file in zipped format, then (as far as I know) yes you would need to specify `zcat` command to open those files through `--readFilesCommand zcat`. There is also another option if you have your files bzip2-compressed, referrer to STAR manual for more. 

As far as specifying out put file/directory you can do that with `--outFileNamePrefix`. For example if you want your newly made BAM file to be named "newBamFile" -> `--outFileNamePrefix newBamFile_` underscore because STAR by default outputs several files where BAM file gets standard post fix "Aligned.out.bam" for unsorted BAM file.

And obviously if you want that "newBamFile_Aligned.out.bam" to be in some other directory just include that in your prefix name. The directory need to be pre made. e.g mkdir bamFiles, then run STAR with `--outFileNamePrefix bamFiles/newBamFile_` 

Referrer to section 3 Running mapping jobs  in the STAR manual for more

Cheers, 

Kirill

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