BWA Alignment

Question

[sara]

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 ?

Answer 1

[GenoMax]

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?

[sara]

single data

[sara]

I tried the lines in the links nothing seem to work, the output is added to the first file.

[GenoMax]

Since you don't show what you actually tried you can see if it was anything like this:

for fastq in *.fq.gz
do
bwa mem bwaIndex/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa $fastq > ${fastq%.*}.bam 
done

[sara]

I tried this line and worked for me, thank you