kallisto abundance estimation

[Sjannie Lefevre]

Hi

I am trying to run abundance estimation with kallisto on 18 samples, using a for loop. I have done this succesfully with RSEM, so that I set a variable $sample, and this is also used as the output prefix (so that I get a .gene and a .isoform file for each sample, without RSEM overwriting the results for every new sample it processes). However, I see now that kallisto have run the first sample, the output is just named "abundance.tsv.genes", without the prefix, so in that way these results will be overwritten, when kallisto continues with the next file. I this an error in the perl script for the kallisto mode?

I know there is the option to add the --samples_file flag, which might be easier when having multiple samples, instead of --single file or --left file and --right file (I am running single end). 

Is it then the entire path that should be added in the third column, if the files are not located in the same folder, or how does it work? Because I assume the purpase of that file is to tell kallisto/rsem/salmon which files to process?

Thanks,

Sjannie

[Brian Haas]

Hi Sjannie,

Try to not use the output prefix option and only use the output directory option.  The output prefix will be dropped in the next release.  Naming the output directories was a better strategy and it fits more easily into the downstream processes of building the expression matrices.

best,

~b

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[Sjannie Lefevre]

Yes - I am running the command now, and I see it makes a directory for each sample, according to the samples.txt file. That is so much easier.

Thanks!

Cheers

Sjannie

On Thursday, 11 May 2017 14:50:38 UTC+2, Brian Haas wrote:

Hi Sjannie,

Try to not use the output prefix option and only use the output directory option.  The output prefix will be dropped in the next release.  Naming the output directories was a better strategy and it fits more easily into the downstream processes of building the expression matrices.

best,

~b

On Thu, May 11, 2017 at 8:11 AM, Sjannie Lefevre <sjannie...@gmail.com> wrote:

Hi

I am trying to run abundance estimation with kallisto on 18 samples, using a for loop. I have done this succesfully with RSEM, so that I set a variable $sample, and this is also used as the output prefix (so that I get a .gene and a .isoform file for each sample, without RSEM overwriting the results for every new sample it processes). However, I see now that kallisto have run the first sample, the output is just named "abundance.tsv.genes", without the prefix, so in that way these results will be overwritten, when kallisto continues with the next file. I this an error in the perl script for the kallisto mode?

I know there is the option to add the --samples_file flag, which might be easier when having multiple samples, instead of --single file or --left file and --right file (I am running single end). 

Is it then the entire path that should be added in the third column, if the files are not located in the same folder, or how does it work? Because I assume the purpase of that file is to tell kallisto/rsem/salmon which files to process?

Thanks,

Sjannie

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[Brian Haas]

Terrific!

-Brian

(by iPhone)

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