I am analyzing data from pseudouridine (https://www.nature.com/articles/nchembio.1836#MOESM157) modifications, where it is reported the position of modified U within cDNA. I need to find the genomic coordinate of this nt in order to get a fasta centered at this point.
The data looks like:
NM_001388,1492,0.1104,0.4,0.425,3' UTR,DRG2
NM_001402,519,0.3298,0.3737,0.3239,CDS,EEF1A1
NM_001402,875,0.41,0.4109,0.353,CDS,EEF1A1
The first and second columns depict NCBI accesion number and cDNA position, respectively.
I tried to find the location using the Ensemble Rest API (https://rest.ensembl.org/documentation/info/assembly_cdna) but the output did not match the correct location. For that I got the Ensemble transcript ID based on the NCBI accesion number.
Thanks.
Hi Manuel,
I don't have access to this paper but can you check the assembly they used in the paper and the one you used in ensembl?
fred
Frederic Lepretre thanks for your answe. They aligned the reads to the human transcriptome (hg19 version). I used the same genomic version to get Ensemble IDs.
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