Commit 62c01919 authored by Charles Girardot's avatar Charles Girardot

readme

parent e6dcce0a
......@@ -9,24 +9,39 @@ The Je tool suite
Contains
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Je currently offers 4 tools :
Je currently offers the following tools :
**je debarcode**
demultiplexs multi-samples fastq files using user-defined input *read-layouts* and write output files following user-defined *output-layouts*.
Replaces both **demultiplex-illu** and **demultiplex** since version 2.0.
**je dropseq**
to process drop-seq results: clips cell barcode and UMI from read 1 and adds them to header of read 2 (a unique output fastq is created).
**je retag**
extracts barcode(s) and UMI sequence(s) embedded in read names of a BAM file and migrate them to proper BAM tags.
**je clip**
to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
removes UMIs contained in reads of fastq files that do not need sample demultiplexing
**je markdupes**
filters BAM files for read duplicates taking UMIs into account.
**je demultiplex**
to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not). Deprecated since version 2.0 (use *je debarcode* instead).
**je demultiplex-illu**
to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
Reads can additionally contain UMIs (inline)
**je markdupes**
Reads can additionally contain UMIs (inline). Deprecated since version 2.0 (use *je debarcode* instead).
to filter BAM files for read duplicates taking UMIs into account
Distributions
......@@ -38,7 +53,7 @@ Source
++++++
src/shell/je
is the wrapper script to call ``java -jar je_1.0_bundle.jar``
is the wrapper script to call ``java -jar je_*_bundle.jar``
src/galaxy/
contains the Je wrappers for Galaxy
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