Hello. I have the sequence of a particular isoform of a gene I'm interested in and I am trying to find out where it is normally expressed in the human body. This sequence was found in cancer cells originally. One suggestion was to use the ucsc genome browser, however that did not prove to be a viable option. The other was to download all of these fastq files from illumina bodymap 2.0 which I did and then I would have to download Bowtie 2.0 and allign 68 of these fastq files using this tool and then convert these alignments into SAM files and then convert these to BAM files and then use an application called "R" to search for my coordinates on this giant map, the problem with this approach is that its going to take a long time due to the speed of the computer I am using and because I am not a bioinformatics person. I was wondering if there was an easier way to find this information. I've tried using NCBI Blast and NCBI SRA blast. Are there any other ways to do this quickly and more efficiently?
Do you know the isoform? Does it have a standard identifier? If not, when you blast your sequence against something like RefSeq, how many hits do you get?
I know the isoform and I have the sequence for it although I do not think this isoform has a standard Identifier because you cannot type the name of the gene into NCBI and get hits for the isoform itself. I did refseq blast and I get two hits on NCBI. I am just trying to find a way to find where it is normally expressed. I found a unigene accession number and also tried to plug that into an application called "TIGER" but unfortunately no data is available for it there either.