how to make short custom reference sequence to use in RNA-seq alignment
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5.1 years ago
genya35 ▴ 40

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 • 1.7k views
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Try it, see what happens.

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

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

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

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Glad to hear you got it working.

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