Till Sauerwein comments

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                                            Till Sauerwein

Use display() not print() to display a dataframe in a jupyter notebook!

I think introducing `display()` is generally a good idea, due to its easier to read output. And a clear tabular output of a DataFrame makes it easier for the human...

Assign libraries for paired end data in the reademption deseq command

Hello @termithorbor It is option a) And thank you for pointing out that the documentation is missing a paired end data example, we will fix this. Best, Till

Unusually high memory memory usage with gene_quanti

We aim to reduce memory consumption in the future. In the meantime there is no other solution than increasing memory. I had a data set with 15 libraries with about...

Unusually high memory memory usage with gene_quanti

yes, it is possible. I implemented printing out timestamps of intermediate steps. If there are still timestamps and intermediate steps added from time to time everything runs as intended. You...

Unusually high memory memory usage with gene_quanti

Which READemption version are you using? Can you check your memory usage? Do you still have memory left?

Unusually high memory memory usage with gene_quanti

all right, there is still some memory left. I would give it a couple more days.

Unusually high memory memory usage with gene_quanti

exactly, the number of maximum parallel processes is the number of maximum number of samples. Is the gene quantification step still running?

docker container without root

Thank you for your making us aware of this issue. I'll double check your solution.

Which normalization from gene_quanti is used for Deseq2?

Hi, The DESeq2 subcommand automatically takes the raw counts from the gene quanti step and there is no option to use normalized counts, since DESeq2 requires raw counts as input....

hello .i have error while align using reademption. im sure about the requirements that i have fullfilled .please check the screenshoots and point me the mistake and solution.

Hi @AzkaSaleem Please add the option --fastq when running the align subcommand. This option needs be turned on when aligning fastq files. Kind regards, Till