BWA Alignment
i'm trying to make bwa i have multiple fastq files and want output of multiple sam files, however, the line does snot seem to work efficiently as it outputs all the data in only the first sam file.
for i in *.fastq.gz; do bwa mem bwaIndex/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa "$i" > $i.sam; done
how can i solve this probelm ?
1 answer
Is this data paired end or single end?
Past threads of interest:
Running BWA mem in a for loop
How to run BWA or the other aligner for paired .fastq in a bash loop and pipeline?
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