In b97jre/RNAmappingPipeline: GBP sequence data throughput

| Key | Value | Comment | |-------|-------|-------| | #Project info | | | | ProjectWD | /Users/johanreimegard/Vetenskap/Data/Wierup/testRun | Give the full path to were the project should be initiated | | metadataTable | /Users/johanreimegard/Vetenskap/Data/Wierup/testRun/metaData.table.tab.txt | The location of the meta data table | | projectID | 20160115 | A unique project ID where the results will end up | | location | UPPMAX | Where the project is run. If 'UPPMAX' paths to scripts will be set and sbatch scripts will be created. UPPMAX is default | | nrOfCores | 16 | Number of cores used. Default is 16 | | #Reads info | | | | readsDir | /Users/johanreimegard/Vetenskap/Data/Wierup/reads | Give the full path to were all the reads are located | | type | PE | PE is paired end reads SE is single end reads. If SE info will be ignored | | sep | 1.fastq.gz 2.fastq.gz | the suffix of the read pairs, eg 1.fastq.gz 2.fastq.gz | | Chemistry | Illumina | Kind of sequencing method. Illumina is default | | readLength | 100 | Length of reads. 100 is default | | readSuffix | fastq.gz | End of reads fastq.gz is default | | #ReferenceInfo | | | | ReferenceFasta | /Users/johanreimegard/Vetenskap/Data/Wierup/references/fasta.fa | Reference sequence file | | ReferenceGTF | /Users/johanreimegard/Vetenskap/Data/Wierup/references/annotation.gtf | | | snakemakeDir | /Users/johanreimegard/git/GBPanalysis/SnakeMakeFiles | Location where all the local snake make files are located | | RscriptsDir | /Users/johanreimegard/git/GBPanalysis/R | Location where all the Rscript files are located | | #Program specific info | | | | #CUTADAPT | | | | #adapterFile | notYetAdded | Fasta file with adapter sequences | | #cutAdaptFlags | notYetAdded | Cutadapt specific parameters | | #STAR | | | | #IF not star reference is added a new one will be generated | | | | STARreference | /full/path/to/reference/STARdir | Should be the star reference build from the fasta and gtf reference above | | STARmappingFlags | | STAR specific parameters | | STABuildFlags | | STAR specific parameters | | #SAMTOOLS | | | | samtoolsViewFlags | -h -bS | STAR specific parameters | | #HTSeq | | | | HTSeqFlags | -t miRNA -i Name -a 0 -f bam -r pos -s yes | STAR specific parameters | | #UPPMAXspecific | | | | projNr | test | Give the correct project number for where the hours should be taken | | time | 1-00:00:00 | Time allocated for the run Default is one day | | email | [e-mail] | The email addres to send if there are any problems with the runs |

b97jre/RNAmappingPipeline documentation built on May 11, 2019, 5:22 p.m.