Commit 734def88 authored by Mathieu Giraud's avatar Mathieu Giraud

tutorial: détails

parent cf870e03
...@@ -375,6 +375,8 @@ expected concentration is 1\% (.01). ...@@ -375,6 +375,8 @@ expected concentration is 1\% (.01).
Then you can set expected concentrations for other clones and you are free to Then you can set expected concentrations for other clones and you are free to
switch between those normalizations. switch between those normalizations.
It is also possible to set up normalization against external data,
contact us if you are interested.
\bigskip \bigskip
...@@ -540,7 +542,7 @@ Therefore the demo account is not suitable. ...@@ -540,7 +542,7 @@ Therefore the demo account is not suitable.
and extract the files from the archive.} and extract the files from the archive.}
You should now have three files. We will imagine that those three files are You should now have three files. We will imagine that those three files are
the results from a single sequencing run. More precisely each corresponds to the results from a single sequencing run. More precisely, each one corresponds to
a single patient. Thus we now want to upload those files and assign all of a single patient. Thus we now want to upload those files and assign all of
them to a same \com{run} and each of them to a single \com{patient}. them to a same \com{run} and each of them to a single \com{patient}.
...@@ -557,13 +559,14 @@ already been created by searching her/his name in the search box at the ...@@ -557,13 +559,14 @@ already been created by searching her/his name in the search box at the
upper left corner upper left corner
\question{ \question{
You are now on the patient, run, set creation page. You are now on the creation page for patients, runs, and sets.
You can create as many patients, runs and sets as you want. You can create as many patients, runs and sets as you want.
\marginpar{Patients, runs and sets are similar: they are all intended to \marginpar{Patients, runs and sets are just different ways to
store samples. The names are just used to add some semantic so that you group samples.
The names are just used to add some semantic so that you
know that your patients will be on the patient page, your runs on the run know that your patients will be on the patient page, your runs on the run
page and your other sets (thus any set of samples you want to make) on the page and your other sets (thus any set of samples you want to make) on the
run page} run page.}
Here we already have a line to create one patient. Here we already have a line to create one patient.
We want to create two additional patients and one run. We want to create two additional patients and one run.
Thus click twice on \com{add patient} and once on \com{add run}. Thus click twice on \com{add patient} and once on \com{add run}.
...@@ -582,7 +585,7 @@ upper left corner ...@@ -582,7 +585,7 @@ upper left corner
} }
\question{ Now you can fill the mandatory fields (circled with red) and, \question{ Now you can fill the mandatory fields (circled with red) and,
optionally the other fields.} optionally, the other fields.}
The last field is optional but it is very important (the field called The last field is optional but it is very important (the field called
\com{patient/run information (\#tags can be used)}. \com{patient/run information (\#tags can be used)}.
...@@ -598,7 +601,7 @@ Also note that you can create other tags just by entering whatever you would ...@@ -598,7 +601,7 @@ Also note that you can create other tags just by entering whatever you would
like in the field preceded with a \#. Thus any tag you enter is saved (and like in the field preceded with a \#. Thus any tag you enter is saved (and
can be suggested later on). can be suggested later on).
\question{For patient 1 in this last field enter \texttt{\#diagnosis of \question{For patient 1 in this last field, enter \texttt{\#diagnosis of
patient with \#B-ALL}. For patient 2, enter \texttt{\#blood sample \#CLL}. patient with \#B-ALL}. For patient 2, enter \texttt{\#blood sample \#CLL}.
For patient 4, enter \texttt{bone \#marrow \#B-ALL}} For patient 4, enter \texttt{bone \#marrow \#B-ALL}}
...@@ -606,7 +609,7 @@ Now the three patients and the run have been created but we have not uploaded ...@@ -606,7 +609,7 @@ Now the three patients and the run have been created but we have not uploaded
the sequence files yet. the sequence files yet.
\question{Now go to the \com{runs} page. You should see the run you have just \question{Now go to the \com{runs} page. You should see the run you have just
created. Click on it. Then click on \com{+add samples}.} created. Click on it. Then click on \com{+ add samples}.}
Similarly to the patient/run creation page, we can add as many samples as we Similarly to the patient/run creation page, we can add as many samples as we
want on this page. want on this page.
...@@ -654,7 +657,7 @@ Instead we will remain on the server. ...@@ -654,7 +657,7 @@ Instead we will remain on the server.
\question{Now go back to the \com{patients} page. You can filter the page \question{Now go back to the \com{patients} page. You can filter the page
using the tags you entered previously. using the tags you entered previously.
Enter \#B-ALL in the search box (notice the autocompletion that helps you) Enter \texttt{\#B-ALL} in the search box (notice the autocompletion that helps you)
and validate with \com{Enter}.} and validate with \com{Enter}.}
\vfill \vfill
......
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