Entering edit mode
4.7 years ago
trumbia
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10
Hello; I have list of nucleotide seq in txt file I want to convert them to geneID (ensembl' uniProt smth offical) Could you help me?
What have you tried? Also, this is a
Questiontype post, not aTooltype post. I've made the necessary change this time, but please be more careful in the future.I have a Deseq2 result and want to integrate this to my model. The problem is deseq result does not have any offical ids ( like someone put x y z) so geneID s does not mean anything but I have sequence of those genes and want to find offical ids. My model has ensemblIDs
Your DESeq2 operation must have used a dataset generated using an RNAseq pipeline that internally used a GTF file. Can you trace the workflow back to the GTF file?
the problem is I used kallisto also my reference genome has same kind of id numbers. (It was someone's work) So I only have their nucleotide seq as smth meaningful.
Please do not use Instant Messaging jargon on a scientific/professional forum.
If sequence is the only data point to go by, you're going to need to use BLAST to figure out the gene that each sequence aligns to with the highest certainty. It might be worth a shot to contact the someone who made the reference genome and check with them for any metadata detail that could help.
It is not possible to contact with that person also I want to ask about blast to you. Is it possible to find all my geneIDs over there since I have 5000id I can not check them by one by. If it is possible do you know any tutorial about it?
Please search the site (and generally on Google also) for command line blast. That should help you query sequences in bulk.