CDR3 characteristics tab

+ +

This tab gives information on the different characteristics of the CDR3.

@@ -51,21 +62,20 @@ text-align:justify;line-height:normal'>Graphs

length distribution of CDR3

Graph visualizing for each donor the distribution of the CDR3 length in amino acids between all sequences.

Amino acid composition of CDR3

Bar graph visualizing for each donor how frequent each amino acid is used in the CDR3 of all sequences. The red colour @@ -74,19 +84,10 @@ ordered from hydrophilic (left) to hydrophobic (right).

D reading frame

- -

Bar graph visualizing the frequency by -which each D reading frame is used in each donor.

- -

Table

Table showing for each donor the median CDR3 length.

diff -r 28fbbdfd7a87 -r b539aeb75980 report_clonality/naive_downloads.htm --- a/report_clonality/naive_downloads.htm Mon Feb 13 09:08:46 2017 -0500 +++ b/report_clonality/naive_downloads.htm Tue Feb 28 08:10:34 2017 -0500 @@ -18,11 +18,6 @@ line-height:115%; font-size:11.0pt; font-family:"Calibri","sans-serif";} -p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing - {margin:0in; - margin-bottom:.0001pt; - font-size:11.0pt; - font-family:"Calibri","sans-serif";} .MsoChpDefault {font-family:"Calibri","sans-serif";} .MsoPapDefault @@ -42,7 +37,14 @@

Downloads +tab

+ +

Description

+ +

The filtered dataset:

The -dataset used to calculate clonality score: Allows you to -download information on V D and J gene usage, the junctions and the amino acid -sequence of the sequences that passed the chosen filter settings. Note: this -file contains all the replicate sequences form the different input files.

- -

The dataset used to generate the CDR3 -length frequency graph: Downloads a table with information used for the -length distribution of CDR3 plot.

Gene +frequencies

The dataset used to generate the distribution of V gene families graph: Downloads a table with information used to generate -the distribution of V gene families graph.

+the distribution of V gene families graph.

Downloads the data used to generate the relative frequency of V gene usage graph. In addition information on the chromosomal order of the V genes can be -found.

+found.

The @@ -95,14 +85,32 @@ style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Downloads the data used to generate the relative frequency of D gene usage graph. In addition information on the chromosomal order of the D genes can be -found.

+found.

The dataset used to generate the relative frequency of J gene usage graph: Downloads the data used to generate the relative frequency of J gene usage graph. In -addition information on the chromosomal order of the J genes can be found.

+addition information on the chromosomal order of the J genes can be found.

+ +

The dataset used to generate the relative frequency of the D +reading frame graph: Downloads +the data used to generate the relative frequency of the D reading frame.

+ +

CDR3 characteristics

+ +

The dataset used to generate the CDR3 +length frequency graph: Downloads a table with information used for the +length distribution of CDR3 plot.

The @@ -113,6 +121,9 @@ Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity in included.

Heatmaps

The data used to generate the VD heatmap for “donor name”:The -data used to generate the DJ heatmap for “donor name”: Downloads the data set used for the generation of the DJ heatmap. For each uploaded donor a separate download is generated.

Circos

A -frequency count of a clonotype: The frequency count of -a clonotype in the unfiltered data set. The clonotype defition used is defined -in the ‘clonal type definition’ filter.

+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The +data used to generate the VD circus plots for “donor name”: +Downloads the data set used for the generation of the VD heatmap. For each +uploaded donor a separate download is generated.

+ +

The +data used to generate the VJ circus plots for “donor name”: +Downloads the data set used for the generation of the VJ heatmap. For each +uploaded donor a separate download is generated.

+ +

The +data used to generate the DJ circus plots for “sample name”: +Downloads the data set used for the generation of the DJ heatmap. For each +uploaded donor a separate download is generated.

+ +

Clonality

+ +

The +dataset used to calculate clonality score: Allows you to +download information on V D and J gene usage, the junctions and the amino acid +sequence of the sequences that passed the chosen filter settings. Note: this +file contains all the replicate sequences form the different input files.

+ +

Sequences +that are present in more than one replicate: Allows you to +download a table containing all the sequences that were present in more than +one replicate. It provides the concidence type, clonaltype, sequence name, +replicate number, and the nucleotide sequence

diff -r 28fbbdfd7a87 -r b539aeb75980 report_clonality/naive_gene_freq.htm --- a/report_clonality/naive_gene_freq.htm Mon Feb 13 09:08:46 2017 -0500 +++ b/report_clonality/naive_gene_freq.htm Tue Feb 28 08:10:34 2017 -0500 @@ -1,103 +1,217 @@ - + - + + + + + - + - +

Gene frequencies tab

This tab gives information on the -frequency of V, D and J gene usage.

+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives +information on the frequency of V, D and J gene usage.

+ +

Graphs

Distribution of V gene families

Distribution of +V gene families

Bar graph showing the frequency -of V gene family usage in all uploaded donors.

Bar graph showing the frequency of V gene family usage +in all uploaded donors.

+ +

Relative frequency of V gene -usage

Relative +frequency of V gene usage

+ +

Bar graph showing the frequency of V genes in all +uploaded donors. The order of the V genes on the x-axis can be altered by +altering the “Order of V(D)J genes +in graphs” filter on the main page of the Immune repertoire pipeline.

Bar graph showing the frequency -of V genes in all uploaded donors. The order of the V genes on the x-axis can -be altered by altering the “Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.

+ +

Relative +frequency of D gene usage

Relative -frequency of D gene usage

Bar graph showing the frequency of D genes in all uploaded donors. The +order of the D genes on the x-axis can be altered by altering the “Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.

+ +

Bar graph showing the frequency of D -genes in all uploaded donors. The order of the D genes on the x-axis can be -altered by altering the “Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.

Relative +frequency of J gene usage

Relative -frequency of J gene usage

Bar graph showing the frequency of J genes in all uploaded donors. The +order of the J genes on the x-axis can be altered by altering the “Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.

+ +

Bar graph showing the frequency of J -genes in all uploaded donors. The order of the J genes on the x-axis can be -altered by altering the “Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.

D +reading frame

+ +

Bar graph visualizing the frequency by which each D reading frame is +used in each donor.

diff -r 28fbbdfd7a87 -r b539aeb75980 report_clonality/naive_junction.htm --- a/report_clonality/naive_junction.htm Mon Feb 13 09:08:46 2017 -0500 +++ b/report_clonality/naive_junction.htm Tue Feb 28 08:10:34 2017 -0500 @@ -1,89 +1,201 @@ - + - + + + + + - + - +

Tables:

Junction +analysis tab

Productive -mean table

Tables:

+ +

The unique +rearrangements are separated in sequences that contain both a +V, D and J gene and sequences that contain only a V and J gene.

Reports for each -donor the number of productive sequences and the mean number of deletions, -N-nucleotides and P-nucleotides. For explanation about the different deletions -and N and P nucleotides see figure above.

Productive mean +tables

Unproductive -mean table

Reports +for each donor the number of productive sequences and the mean number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.

+ +

Unproductive +mean table

Reports for each -donor the number of unproductive sequences and the mean number of deletions, -N-nucleotides and P-nucleotides. For explanation about the different deletions -and N and P nucleotides see figure above.

Reports +for each donor the number of unproductive sequences and the mean number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.

Productive -median table

Productive +median table

Reports for each -donor the number of productive sequences and the median number of deletions, -N-nucleotides and P-nucleotides. For explanation about the different deletions -and N and P nucleotides see figure above.

Reports +for each donor the number of productive sequences and the median number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.

Unproductive -median table

Unproductive +median table

Reports for each -donor the number of unproductive sequences and the median number of deletions, -N-nucleotides and P-nucleotides. For explanation about the different deletions -and N and P nucleotides see figure above.

Reports +for each donor the number of unproductive sequences and the median number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.

diff -r 28fbbdfd7a87 -r b539aeb75980 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Mon Feb 13 09:08:46 2017 -0500 +++ b/report_clonality/r_wrapper.sh Tue Feb 28 08:10:34 2017 -0500 @@ -325,7 +325,7 @@ echo "" >> $outputFile while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median do - echo "" >> $outputFile + echo "" >> $outputFile done < $outputDir/junctionAnalysisUnProd_median_nD.txt echo "

Unproductive median
Donor	Number of sequences	V.DEL	P1	N	P2	DEL.J	Total.Del	Total.N	Total.P	Median.CDR3
$Sample	$unique	$VDEL	$P1	$N1	$P2	$DELJ	$TotalDel	$TotalN	$TotalP	-/td>
$Sample	$unique	$VDEL	$P1	$N1	$P2	$DELJ	$TotalDel	$TotalN	$TotalP	-

" >> $outputFile