FASTA and FASTQ examples

Question

[dshulgin]

Hi everyone. Fisrt of all, i'd like to say sorry for that silly question.

I want to test STAR aligner, so i need a test data.

Where i could download reads and reference genome to do that? And it should be small for better understanding what i will get. I didn't find any small files for that.

Thanks.

Answer 1

[Antonio R. Franco]

You can download reads from the NCBI SRA database. You will have the choice to download only small sequences, or to extract from a file, a portion of it to make it small. It is up to you

[dshulgin]

Thanks, finally i've found out how to download without installing SRA toolkit etc.

Answer 2

[h.mon]

On the Subread package (which is another mapper/aligner worth of consideration) there is a "test" folder, with small fasta and fastq files.

[dshulgin]

Thanks, didn't know about that.

Answer 3

[Dan D]

You could also create simulated data.