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Convert gene list to fasta file

Hello,

I have a gene list with 504 genes and I want to convert them to fasta file, because I want to do alignment some NGS data with only these genes. How could I do that?

Thanks

next-gen alignment
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updated by theobroma22 theobroma22 • written by nickmarinakis92 • nickmarinakis92

504 genes from a single organism? Post a few examples if you want further help.

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written by GenoMax GenoMax

This doesn't sound like a good idea. Why would you want to align to just these genes?

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written by WouterDeCoster WouterDeCoster

Because these genes are connecting to a specific phenotype

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written by nickmarinakis92 • nickmarinakis92

I don't think that reason justifies aligning just to those. If you align to a subset of the genome you will get false positive alignments. Always align NGS to the full genome.

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written by WouterDeCoster WouterDeCoster

You can always extract the reads aligning to a position on the genome/genes (e.g. with samtools, bedtools, featurecounts, deeptools ... many) once all the reads are aligned to whole genome. If you remove the possibility for a read to align to a best position on the genome, it will be forced to align (or discarded) to a position where it doesn't belong. This introduces a lot of noise in your data.

I'm really curious to know what would you do in downstream analysis after aligning to only these 504 genes. Would you go for differential analysis with this set?

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written by venu venu

1 answer

Assuming you have the sequences and you can use R, in R you can use the write.fasta() command which is in the seqinr package.

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written by theobroma22 theobroma22

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