diff --git a/docs/alignment/bisulfite/BALv1.xml b/docs/alignment/bisulfite/BALv1.xml new file mode 100644 index 0000000..dee515a --- /dev/null +++ b/docs/alignment/bisulfite/BALv1.xml @@ -0,0 +1,237 @@ + + + + BAL + 1 + + Charles Imbusch + c.imbusch@dkfz.de + + + + * trimming, in silico conversion of reads, mapping, re-converting reads, flagstats, QC after mapping + + + + + SampleID_R1 + FASTQ + single + raw input file, pre-filtered for Illumina chastity filter failed reads + + + SampleID_R2 + FASTQ + single + raw input file, pre-filtered for Illumina chastity filter failed reads + + + + + + + reference_genome + FASTA + single + The in silico bisulfite converted reference genome file + + + reference_genome.pos + text + single + CG/GH positions in the reference genome created by 'methylCtools fapos' + + + + + + + DEEPID.PROC.DATE.aln + BAM + single + Final Bam file with reconverted Cs + + + DEEPID.PROC.DATE.idx + BAI + single + Corresponding BAM index file + + + DEEPID.PROC.DATE.R1.aln + SAI + single + aligned reads, output from bwa + + + DEEPID.PROC.DATE.R2.aln + SAI + single + aligned reads, output from bwa + + + DEEPID.PROC.DATE.R1.trim + FASTQ + single + Adaptor trimmed fastq file + + + DEEPID.PROC.DATE.R2.trim + FASTQ + single + Adaptor trimmed fastq file + + + DEEPID.PROC.DATE.R1.conv + FASTQ + single + In silico converted fastq file + + + DEEPID.PROC.DATE.R2.conv + FASTQ + single + In silico converted fastq file + + + DEEPID.PROC.DATE.flagstats + text + single + samtools flagstat + + + DEEPID.PROC.DATE.PicardMarkDupmetrics + text + single + + + + DEEPID.PROC.DATE.PicardInsertSizemetrics + text + single + + + + DEEPID.PROC.DATE.CHROM_CG_CH.mcall + methylation calls + collection + The methylation calls separated per chromosome + + + DEEPID.PROC.DATE.CHROM_CG_CH.mcall.tbi + tabix index + collection + The tabix index for the methylation calls of each chromosome + + + DEEPID.PROC.DATE.CHROM_CG_CH.mcall.metrics + text file + collection + Metrics for methylation calls of each chromosome + + + DEEPID.PROC.DATE.reconversion.metrics + text + single + Metrics on re-conversion + + + + + + seqprep + 0.4 + + SampleID_R* + trim reads by default adaptor + + + methylCtools + 0.9.2 + + DEEPID.PROC.DATE.R*.trim + bisulfite convert reads in silico + + + bwa + cnybwa-0.6.2 + {DEEPID.PROC.DATE.R*.aln} ]]> + DEEPID.PROC.DATE.R*.conv + produce two intermediate .sai files per lane, performed on convey machines + + + bwa + 0.6.2-tpx + + sampe_output + ]]> + + DEEPID.PROC.DATE.R*.aln + pairing of reads to SAM format; output is piped to next step + + + methylCtools + 0.9.2 + + sampe_output + Input piped from previous step; reconversion step of methylCtools + + + samtools + 0.1.19 + + no looping + Sorting BAM by coordinate + + + Picard + 1.61 + + + + no looping + Merging lanes, marking duplicates and index creation. The Picard commandline gets I=bamfile for each bam file as input which is simplified above in the command line. + + + samtools + 0.1.19 + {DEEPID.PROC.DATE.flagstats} ]]> + no looping + + + + Picard + 1.61 + + + + no looping + creates several output files + + + methylCtools + 0.9.2 + + + + CHROM + Creates methylation calls for each chromosome + + +