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I have a bunch of (human) Agilent probes (both probe ID and the actual sequence, some custom array), and I would like to get the hgnc gene symbol based on the actual probe sequences, rather than the IDs (I can use the ID to get hgnc gene symbol, but I want to match the actual probe sequence).

What I would like is some CLI way of

  1. submitting all probes (as a fasta file?)
  2. getting the hgnc gene symbol for each probe based on the best alignment

with either a way of specifying an alignment threshold before, or getting hgnc gene symbol and some alignment quality score so I can prune out the bad hits.

I can do all of the above interactively, but the probes are more than 200K, so I need an automated CLI way.

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  • $\begingroup$ I am aware I could build some multi step approach, but I was wondering whether there is a tool that lets me tool myfastfile local_or_remote_reference --just_spit_out_hgnc --alignment_score $\endgroup$ Feb 23 at 10:07

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