Question: The nucleiotide sequence to gene id
0
gravatar for trumbia
4 weeks ago by
trumbia10
trumbia10 wrote:

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?

rna-seq • 112 views
ADD COMMENTlink modified 4 weeks ago by RamRS24k • written 4 weeks ago by trumbia10

What have you tried? Also, this is a Question type post, not a Tool type post. I've made the necessary change this time, but please be more careful in the future.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by RamRS24k

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

ADD REPLYlink written 4 weeks ago by trumbia10

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?

ADD REPLYlink written 4 weeks ago by RamRS24k

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.

ADD REPLYlink written 4 weeks ago by trumbia10

smth

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.

ADD REPLYlink written 4 weeks ago by RamRS24k

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?

ADD REPLYlink written 4 weeks ago by trumbia10

Please search the site (and generally on Google also) for command line blast. That should help you query sequences in bulk.

ADD REPLYlink written 4 weeks ago by RamRS24k
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