how to make short custom reference sequence to use in RNA-seq alignment

Question

[genya35]

Hello,

I would like to align reads from RNA fastq to a custom short reference sequence. I made a small fasta file with >Name in the header followed by DNA sequence. Do I need to do anything else to the file for tools lie BBmap or HISAT2 to be able to use it as a reference?

Thanks

[st.ph.n]

Try it, see what happens.

[genya35]

it didn't work with BBmap but I will try a different aligner, perhaps?

[st.ph.n]

Post your command, and the error (if any), and perhaps an example of your FASTA.

[genya35]

I got it to work with HiSAT2 and it's awesome!

[st.ph.n]

Glad to hear you got it working.