Filter out reads mapped to specific sequences¶
Input¶
1. fastq.tsv¶
3 columns: R1, R2, sample_name
You can prepare your fastq.tsv using run_lsf.py --guess_input
2. your fasta file¶
standard fasta file
>chrM
AAAAAAAAAAAAAAAAA
Usage¶
# login to a compute node
hpcf_interactive.sh
run_lsf.py -f fastq.tsv -p filter_reads --my_fasta test.fa
Output¶
Newly generated fastq files without those unwanted reads are stored in the jid folder (e.g., filter_reads_yli11_2022-05-13).