This will be generated in the first step. You can copy the table given below and paste them into excel and fill in all the information there. Most of the parameters are fine and you do not need to change them.
The ones you need to change are
readsDir
suffix
fastq.gz
type
sep
type
is PE then it should be the end of the reads. Common ones are:1.fastq.gz 2.fast.gz
_R1_001.fastq.gz _R2_001.fastq.gz
type
is SE it can be removedReferenceFasta
ReferenceGTF
An example of a table is given below. It is also possible to copy the table below into excel, make the changes there and save it as a tab delimeted file called parameters.table.txt
. Make sure that you afterwards convert the format of the file to unix format
Even though I recomend filling out the parameter table using vim
or emacs
in the terminal it is possible to do it in excel. This is how you do that:
parameters.table.txt
This table contains all samples with their corresponding reads. It also contains all the meta data for all the samples that will be used later to analyse the data. Try to add as much meta data as possible to identify reasons for differences in the data. Before running the pipelie do the following steps in the meta data table.
It is also possible to copy the table below into excel, make the changes there and save it as a tab delimeted file called metadata.table.txt
. Make sure that you afterwards convert the format of the file to unix format.
This is how you do that:
metadata.table.txt
from the working directory. metadata.table.txt
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