check sample barcode frequency in index reads¶
barcode_frequency.py [Undertermined_R1.fastq.gz]
Usage¶
barcode_frequency.py Undertermined_R1.fastq.gz
Output¶
1. Barcode_count_table.csv¶
This is usually what we need. A sorted frequency table for each barcode pair.
2. Barcode_raw_table.csv¶
Raw read names and barcode table.
Barcode frequency in 5’-end¶
create a working dir and copy your Undetermined_S0_R1_001.fastq.gz here.
gunzip Undetermined_S0_R1_001.fastq.gz
module load homer/4.10
homerTools barcodes 8 Undetermined_S0_R1_001.fastq -min 1
By default, homer checks the first 8bp frequency and output each 8bp to a file.