用bowtie2、samtools...的代码
if you wanna use(must load) the file.fastq to alig to other reference file.fasta（load from the NCBI)
[bowtie2]
$$bowtie2-build reference.fasta ref # become 6 binary file
[bowtie2][samtools]
$$bowtie2 ( –end-to-end ) -x ref -U file.fastq -S file.sam # make a file.sam & -end-to-end means “Gobal alignment”
$$samtools view -Sb file.sam > file.bam # make a file.bam
$$samtools sort file.bam file_sorted # make a file_sorted.bam
maybe make a file.bed
[bedtools]
$$bedtools bamtobed file.bam > file.bed
LOOP：
for i in 00{1..8}.fastq;
do name=${i%.fastq};
bowtie2 -p 4 -x cd119 $name.fastq -S $name.sam && samtools view -Sb $name.sam -o $name.bam && samtools sort $name.bam $name.sort && samtools index $name.sort.bam;
done
SUPER LOOP:
#Array of fastq
arrayFastq=(01 02 03 04 05 06 07 08 09 10 11 12 13 14 15)
#Array of fasta
arrayFasta=(CDMH1 phiCD38-2)
for a in ${arrayFasta[@]}
do
for q in ${arrayFastq[@]}
do
echo "Aligning "${q} "to "${a}" ..."
filename=${a}"_"${q}
bowtie2 -x ${a} -U ${q}.fastq -S ${filename}.sam && samtools vie w -Sb ${filename}.sam -o ${filename}.bam && samtools sort ${file na me}.bam ${filename}.sort && samtools index ${filename}.sort.b am
echo -e "Finished\n"
done
done
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