STAR read Mapping

[NDUFB11]

Hello everybody,

I kindly need your help again ...

I want to map my reads on the genome using STAR but for some reason I get an error that I don't know how to solve

When I type the command line here is what I get:

Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq.zip clipped/ SRR359063_2.fastq.zip --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate --readFileCommand gunzip

EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "readFileIn" in input "Command-Line-Initial"
SOLUTION: use correct parameter name (check the manual)

Feb 19 18:49:56 ...... FATAL ERROR, exiting[/B]

I also tried to process unzipped files and remove the command to execute each single input file --readFileCommand, but still I can't go further,

I have a MacOs terminal,


thank you

Patrizio

[GenoMax]

STAR requires a lot of RAM depending on genome size. e.g. human genome will need ~30G of free RAM which you may not have available on your Mac. If that is true, you will not be able to do this on your local mac.

[NDUFB11]

Do you think that this is the reason why I have this error? this is a nematode genome so I thought the process would have been faster than human

I will scan the command, I found an error probably I didn't type correctly the command

later I will also try with topHat, it should be feasible because requires less RAM

thank you

[GenoMax]

Oops. I should have looked at the error carefully. You are correct.

Edit: Found the problem. You have a space between clipped and file name here (clipped/ SRR359063_2.fastq.zip ). Remove that.

[NDUFB11]

It's working !!!! holeee'!

have a look

Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq clipped/SRR359063_2.fastq --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate 
Feb 19 19:22:44 ..... started STAR run
Feb 19 19:22:44 ..... loading genome
Feb 19 19:22:49 ..... started mapping
Feb 19 19:23:50 ..... finished mapping
Feb 19 19:23:50 ..... started sorting BAM
Feb 19 19:23:54 ..... finished successfully
Patrizios-MBP:processing patrizio$

I can go further with the process !

Thank you GenoMax

at some point I will ship a bottle of wine to you

-P

[GenoMax]

Looks good!

[yoderto]

Just a quick comment-- STAR does come with RAM limiting arguments: --limitGenomeGenerateRAM, --limitIObufferSize , --genomeSAsparseD