Analyse UMI using picard's ExtractIlluminaBarcodes & IlluminaBasecallsToSam with 2 or 4 lanes

Question

[User000]

Hello

I am analysing UMI using this tutorial

I know that both ExtractIlluminaBarcodes & IlluminaBasecallsToSam process one lane at a time. What if I have 2/4 lanes (for example L001, L002, L003, L004) ? Should I run ExtractIlluminaBarcodes & IlluminaBasecallsToSam for each lane separately and then merge the BAM files?

This is my command lines:

java -jar picard.jar ExtractIlluminaBarcodes BASECALLS_DIR=/bcl/MY_RUN/Data/Intensities/BaseCalls/ LANE=1 READ_STRenter code hereUCTURE=101T8B9M8B101T BARCODE_FILE=barcodes.txt METRICS_FILE=metrics_output.txt OUTPUT_DIR=barcodes

java -jar picard.jar IlluminaBasecallsToSam BASECALLS_DIR=/bcl/MY_RUN/Data/Intensities/BaseCalls/ BARCODES_DIR=barcodes LANE=001 READ_STRUCTURE=101T8B9M8B101T RUN_BARCODE=run1 LIBRARY_PARAMS=library.txt MOLECULAR_INDEX_TAG=RX ADAPTERs_TO_CHECK=INDEXED READ_GROUP_ID=BO NUM_PROCESSORS=2 IGNORE_UNEXPECTED_BARCODES=true > barcodes.log