# HG changeset patch
# User davidvanzessen
# Date 1482396182 18000
# Node ID 3ef457aa5df6bf14c7e243da2547cbb3cf104f8c
# Parent 5d11c9139a55d535cec30cad583abf502cf35e7d
Uploaded
diff -r 5d11c9139a55 -r 3ef457aa5df6 complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml Wed Dec 21 11:53:03 2016 -0500
+++ b/complete_immunerepertoire.xml Thu Dec 22 03:43:02 2016 -0500
@@ -128,13 +128,13 @@
**Input files**
IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM & CSR pipeline can be used as input files.
-Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
+Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded replicates as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
-----
**Donor and replicates**
-The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one sample can be uploaded. However, multiple samples per donor can be uploaded by using the insert sample button. In addition, multiple donors van be added by using the insert donor button. The multiple sample option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 samples have to be included per donor.
+The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one replicate can be uploaded. However, multiple replicates per donor can be uploaded by using the "Add new replicate" button. In addition, multiple donors van be added by using the insert donor button. The multiple replicate option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 replicates have to be included per donor.
-----
@@ -156,7 +156,7 @@
**Species**
-Enter the species of the sample you would like to analyse.
+Enter the species of the replicates(s) you would like to analyse.
-----
@@ -174,7 +174,7 @@
**Shared clonal types / clonality**
-This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a sample no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
+This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a replicate no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
-----
diff -r 5d11c9139a55 -r 3ef457aa5df6 report_clonality/naive_compare.htm
--- a/report_clonality/naive_compare.htm Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/naive_compare.htm Thu Dec 22 03:43:02 2016 -0500
@@ -49,7 +49,7 @@
By ticking the include box of a donor, the three
heatmaps of this donor is visualized underneath eachother. By clicking the
-include box of multiple samples the heatmaps of these samples are visualized
+include box of multiple replicates the heatmaps of these replicates are visualized
next to each other allowing easy comparison of heatmaps.
diff -r 5d11c9139a55 -r 3ef457aa5df6 report_clonality/naive_downloads.htm
--- a/report_clonality/naive_downloads.htm Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/naive_downloads.htm Thu Dec 22 03:43:02 2016 -0500
@@ -129,7 +129,7 @@
The
-data used to generate the DJ heatmap for sample name:
Downloads the data set used for the generation of the DJ heatmap. For each
uploaded donor a separate download is generated.
diff -r 5d11c9139a55 -r 3ef457aa5df6 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/r_wrapper.sh Thu Dec 22 03:43:02 2016 -0500
@@ -37,7 +37,7 @@
echo "Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)
" > $2
echo "" >> $2
-echo "| Sample/Replicate | All | Productive | Unique Productive | Unproductive | Unique Unproductive |
|---|
" >> $2
+echo "| Donor/Replicate | All | Productive | Unique Productive | Unproductive | Unique Unproductive |
|---|
" >> $2
while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
do
echo "| $sample | " >> $2
@@ -48,7 +48,7 @@
echo "$unproductive_unique (${perc_unprod_un}%) |
" >> $2
done < $outputDir/productive_counting.txt
echo "
" >> $2
-echo "Table showing the number and percentage of (unique) productive and unproductive sequences per sample and per replicate.
" >> $2
+echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate.
" >> $2
echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
echo "" >> $2
@@ -138,7 +138,7 @@
echo "
" >> $outputFile
echo "" >> $outputFile
-echo "| Sample | Median CDR3 Length |
|---|
" >> $outputFile
+echo "| Donor | Median CDR3 Length |
|---|
" >> $outputFile
while IFS=, read Sample median
do
echo "| $Sample | $median |
" >> $outputFile
@@ -242,6 +242,8 @@
echo "| Sum | $readsSum |
" >> $outputFile
done < $outputDir/ReplicateSumReads_$sample.csv
+ echo " | |
" >> $outputFile
+
#overview
echo "| Number of replicates containing the coincidence | Number of sequences shared between replicates |
" >> $outputFile
while IFS=, read type count weight weightedCount
@@ -280,28 +282,28 @@
echo "" >> $outputFile
echo "
" >> $outputFile
- echo "
Productive mean| Sample | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
+ echo " Productive mean| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
do
echo "| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
" >> $outputFile
done < $outputDir/junctionAnalysisProd_mean.csv
echo "
" >> $outputFile
- echo " Unproductive mean| Sample | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
+ echo " Unproductive mean| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
do
echo "| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
" >> $outputFile
done < $outputDir/junctionAnalysisUnProd_mean.csv
echo "
" >> $outputFile
- echo " Productive median| Sample | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
+ echo " Productive median| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
do
echo "| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
" >> $outputFile
done < $outputDir/junctionAnalysisProd_median.csv
echo "
" >> $outputFile
- echo " Unproductive median| Sample | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
+ echo " Unproductive median| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|
" >> $outputFile
while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
do
echo "| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
" >> $outputFile