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UMI_kit

parsing RNA-seq data with Unique Molecular Identifiers (UMI)

Usage

  1. Sequencing adapter trimming

  2. UMI barcode, following G, and 3' poly-(A) trimming

    UMI_trim.pl yoursample.fastq.gz yoursample

  3. Read mapping to genome

  4. Converting bam to bed

    bamToBed -bed12 -i yoursample.bam | awk -vOFS='\t' '{split($4,a,/=/); $4=a[2]; print $0}' | gzip > yoursample.bed.gz

  5. UMI collapse

    UMI_collapse.pl yoursample.bed.gz yoursample.UMI_collapsed.bed.gz

  6. UMI deduplicates

    UMI_dedup.pl yoursample.UMI_collapsed.bed.gz yoursample.UMI_dedup.bed.gz

Contact

xi.wang (at) dkfz-heidelberg.de