Hi every one i was trying to mapping multiple fastq files with multiple references in a single batch mode. for this i did like this
# make an index of our all resequences file for file in ./*.fasta do echo $file bwa index $file done #Now take two fastq file and start bwa mem for mapping for read in./*.fastq do echo $read bwa mem $file $name $name > $aln.sam done
The problem here for input two fastq file one after another. for example my .fastq file name like this
Only difference in R1/R2 can anyone help me for this coding how can i take input two file one after another according to name
Thank you advance.