Alignment fastq files

Alignment fastq files

0

I have a question. I need to align and convert fastq files (unpaired) into bam file. If to beo sure I need to ast first if this command below are enough to do this or I forgot about something.

bowtie2 -x input.index.hg19 -U input.fastq -S {output}

and then:

samtools view -u input.sam -o output.bam

If it is something that I forgot, (what I need to take int consideration) I ask because my further pipeline does not work like it should.

Kindly help.


bowtie2


samtools


alignemnt

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