Where can I find a fasta file with RefSeq Select sequences?

Question

[rjd254]

I have found in gencode and ucsc multiple different refseq RNA sequences, but while I see the pages on NCBI explaining RefSeq Select (https://www.ncbi.nlm.nih.gov/refseq/refseq_select/#Accessing_Select) I don't see a way to download a fasta of these sequences. I'm trying to make a script that checks for off target effects in RNA and having a nonredundant set of mRNA would be very helpful. Is there somewhere to download this that I'm missing? Or is there some code to generate it from the existing refseq mRNA sources? I really appreciate your help!

Answer 1

[GenoMax]

Using Entrezdirect:

$ esearch -db nucleotide -query "Refseq_select[filter]" | efetch -format fasta | grep ">" | head -5
>NM_001387263.1 Homo sapiens PAT1 homolog 2 (PATL2), transcript variant 6, mRNA
>NM_001354886.2 Homo sapiens uncharacterized LOC100129484 (LOC100129484), mRNA
>NM_001123364.3 Homo sapiens methyltransferase like 24 (METTL24), transcript variant 1, mRNA
>NM_001271907.2 Homo sapiens spermatogenesis associated 33 (SPATA33), transcript variant 1, mRNA
>NM_001135580.2 Homo sapiens chromosome 19 open reading frame 71 (C19orf71), mRNA

You could add terms to limit search as needed and then save the results to a file

$ esearch -db nucleotide -query "Refseq_select[filter]" | efetch -format fasta > seq.fa

[rjd254]

Wow, haven't seen this before, seems perfect! Now is there a way to add MANE too or should those be included in RefSeq Select? Maybe I can just download them both and merge them if they're exclusive. Also I tried installing it and got this error

Can't locate IO/Socket/SSL.pm in @INC (you may need to install the IO::Socket::SSL module

I'm new to perl, is there an easy way to fix this? Otherwise the installation seemed okay.

[GenoMax]

Use conda to install. That would be the easiest. I will need to look at MANE. Will try that tomorrow.