TCR

A pipe for extracting TCRs from RNAseq data.

To start a new analysis run the following commands

1. Optionally start with:
   scripts/TCRcaller init <pathToAnalysis>
   to create folders and database structures logfile etc.

2. Then run the add sample command to add a sample id/name
   scripts/TCRcaller addSample <pathToAnalysis> <sampleName>

3. When a sample has been added it's time to add some data to that sample either by adding a pair of fastq files by the following command:
   scripts/TCRcaller addFastq <pathToAnalysis> <sampleName> <read1file> <read2file>
   or by adding a single fastq file:
   scripts/TCRcaller addFastq <pathToAnalysis> <sampleName> <singleReadsFile>

4. If its the first time the analysis is run on the system you will need to download the tools needed this can be done by adding the term getTools anywhere on the commandline eg:
   scripts/TCRcaller getTools <pathToAnalysis> <sampleName>

5. Additionally a bowtie2 reference with TCR sequences is needed for the alignment to work. The software automatically uses the latest created/changed reference file matching the following pattern references/*.fa. Either you create your own reference or add the term getReferences anywhere on the commandline to download the latest sequences from NCBI and build a bowtie2 index. For example like this:
   scripts/TCRcaller getTools <pathToAnalysis> <sampleName> getReferences
   to both download tools and create a bowtie2 reference in one step.

6. Finally to tell the software to do some work run the following command:
   scripts/TCRcaller findTCR <pathToAnalysis>

Have fun!!
and tell me what you want next ;)
//EB