Is there a way to map an entire directory of reads at once? Would I just have to write a script for this specific to my directory structure and data? I'm using BWA MEM to map 49 paired-end reads and have been going 1-by-1, using this line to pipe to samtools:
srun -c 8 --mem 15000 -t 2:00:00 bwa mem -t 8 /projects/tollis_lab/crocs/data/ref_genome/AllMis/GCF_000281125.3_ASM28112v4_genomic.fna /projects/tollis_lab/crocs/analysis/reads_to_map/HC02-USNM42150_1P.fastq.gz /projects/tollis_lab/crocs/analysis/reads_to_map/HC02-USNM42150_2P.fastq.gz | samtools view -hb | samtools sort -l 5 -o /projects/tollis_lab/crocs/analysis/bams_P_AllMis/HC02-USNM42150_C.sp_AllMis_sp.bam
I'm still a newbie so not sure if mapping individually is necessary or there's a much faster way to do it, but I'm mapping to 3 different reference genomes so if there is a faster way I would love to know.