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tgirke / systemPipeR

Project Website:
http://girke.bioinformatics.ucr.edu/systemPipeR
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Not getting the Bam files #68

Closed ishaaq34 closed 2 years ago

ishaaq34 commented 2 years ago

I managed to run that but I could not get bam files. I only got the sam files.

toshow

Could you please help out here . @dcassol

dcassol commented 2 years ago

You need to explicitly request that in the runCommandline() function. 

?runCommandline
args <- runCommandline(args, make_bam = TRUE, del_sam=FALSE, dir = TRUE)

Here you have 3 main possibilities: 1) to detect SAM file outputs and convert them to sorted and indexed BAM files; 2) Keep the sam files; 3) to create a subfolder for all the outputs or not.

dcassol commented 2 years ago

Hello @ishaaq34, I'm going to close this for now! Feel free to re-open if you have any additional questions. Cheers, Daniela