Tool for pre-processing alignments with barcode

• Python 2.7.10 or later

• pysam 0.12 or later

1. Trim clipped reads

   python ./x_toolbox.py -T -b input.sorted.bam -r ${REF_FILE} -o output_trimmed.bam -p ./tmp -n 11

2. Convert reference indexed alignment to barcode (BX) indexed alignments

   python ./x_toolbox.py -C -b input.sorted.bam -o output_barcode_indexed.bam -p ./tmp -n 11

3. Convert reference indexed alignment to molecule barcode (MI) indexed alignments

   python ./x_toolbox.py -X -b input.sorted.bam -o output_barcode_indexed.bam -p ./tmp -n 11

4. Convert barcode indexed alignments to reference based alignment

   python ./x_toolbox.py -K -b input.sorted.bam -i header_template_bam.bam -o output_barcode_indexed.bam

5. Haplotype block statistic

   python ./x_toolbox.py -B -b input.sorted.bam -o block_info.txt -n 11 -p ./tmp/

6. Molecule length statistic

   python ./x_toolbox.py -S -b barcode_indexed_sorted.bam -o molecule_info.txt -n 11 -p ./tmp/

7. Generate barocde matrix

   python ./x_toolbox.py -G -b input.sorted.bam -i chrom_size.txt -o out_matrix.bed -n 11 -p ./tmp/ -w 10000 -k 250 -m 1

   Matrix visualization: The exported matrix can be viewed through HiGlass: NA12878 10X hg19

• Generate matrix by haplotype information, for each block generate two matrices