bowtie2 tools and reads targeting

Question

[doramora]

Hi! I need to target some reads on my sequence and then i need to pick up reads from there as fastq. has bowtie2 such tools, or i need some other programms to do?

[lieven.sterck]

so you want to align reads to a certain region and want to output the matching reads again in fastq format?

BBMap will be able to do this easily. (as do other software likely)

[doramora]

ok, thank you! and when it'll save my reads as .sam i should simply use samtools in terminal, or BBMap has some othee tools to save it in fastqc?

[lieven.sterck]

BBMap has a gazillion options, likely there is one to output the reads directly in fastqc rather than in sam and then convert them. (most of the time it will look at the file extension to determine the format)