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UCSC-LoweLab / tRAX

tRNA Analysis of eXpression
GNU General Public License v3.0
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Location of BAM files if already pre-mapped #4

Closed emm13 closed 3 years ago

emm13 commented 4 years ago

Hi Andrew,

Thank you for your lovely piece of software and really easy to follow set of instructions. I am doing a custom mapping of my samples and want to provide these custom BAM files to your analysis pipeline for downstream tRNA stats.

From what I can see the option "--lazyremap" should do this but I don't know how to indicate to the scripts as to where my BAM files are. Intuitively, this would be in the samples.txt file. I tried replacing the fastq files with BAM files and that didn't work. I have tried a couple of directories of BAM files - one in the running directory and one where the fastq files are and neither works. The script just remaps the entire set again.

I'm sorry if I'm being a bit stupid here and overlooking something obvious. Could you please advise on how to proceed ?

andrewdholmes commented 4 years ago

The bam files are put in the current working directory and are named with the sample name (first field in the samples.txt file) followed by .bam.

They also should have a @PG bam header line with " PN:TRAX" in it, but if that's missing then the whole program should just abort early, not overwrite.

Andrew Holmes

On Fri, Nov 29, 2019 at 4:50 AM Emm13 notifications@github.com wrote:

Hi there,

Thank you for your lovely piece of software and really easy to follow set of instructions. I am doing a custom mapping of my samples and want to provide these custom BAM files to your analysis pipeline for downstream tRNA stats.

From what I can see the option "--lazyremap" should do this but I don't know how to indicate to the scripts as to where my BAM files are. Intuitively, this would be in the samples.txt file. I tried replacing the fastq files with BAM files and that didn't work. I have tried a couple of directories of BAM files - one in the running directory and one where the fastq files are and neither works. The script just remaps the entire set again.

I'm sorry if I'm being a bit stupid here and overlooking something obvious. Could you please advise on how to proceed ?

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emm13 commented 4 years ago

Dear Andrew,

Super - thanks so much for your quick reply!

Manasa