Question: how to make short custom reference sequence to use in RNA-seq alignment
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gravatar for genya35
18 months ago by
genya3510
genya3510 wrote:

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

reference sequence • 688 views
ADD COMMENTlink written 18 months ago by genya3510

Try it, see what happens.

ADD REPLYlink written 18 months ago by st.ph.n2.4k

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

ADD REPLYlink written 18 months ago by genya3510

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

ADD REPLYlink written 18 months ago by st.ph.n2.4k

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

ADD REPLYlink written 18 months ago by genya3510

Glad to hear you got it working.

ADD REPLYlink written 18 months ago by st.ph.n2.4k
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