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List of sequences to gene symbol

Hi!

I have list of probes matching genes. I have already written an R code using BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db. The code is working fine, however it takeas a long time to check all probes. What are other possible ways to solve this problem?

mapping
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written by catechize.2.learn catechize.2.learn

Where/what are the probes from? What does your code look like?

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written by jared.andrews07 jared.andrews07

loop over probes; loop over chromosome

    matchPattern > create  Grange > genes [finOverlaps with genes from TxDb.Hsapiens.UCSC.hg19.knownGene] > find symbol > break chromosome loop

Probes contain:

GAGATAACTAGAACAGTGTCCCTCCCCTTTTATAACCTGTGTTTTTAGATTTCAAAAAGA CTAACTGTCAAACAAAGATGGGCTAATTAAACGGATGCCAACTAATCGGAAAACTTCTGG CCAGAAGCTCCAGCATGGTCCACCTACCAGAAGCTCCAGCATGATTTACCCATGAGTAGC TAAGTACGGTAATGCAAGAAGGTGCAGCAGGCGTAGTGCATTACAGCAACACTGAAAAAC TATGAGAGATGAAGAGATAAGGTCTAACTGTTACCTGGGCTGAACCCTTGGACTTCTAGG CAGTAGCGAGTATTTACTAAGTACTTTCTATTTGCGAGGCCCTGATAAAAGTACTGTCCT ~ 5600

I am not familiar with RNAseq but I guess one can use HISAT2 or Rsubread to perform this quickly.

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written by catechize.2.learn catechize.2.learn

Suggesting an alternative. If all you are doing is checking where probes map on hg19 you could use blat (which is perfectly suited for this purpose). You can download it here.

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written by GenoMax GenoMax

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