3'UTR viewing in IGV or other browser

Question

[kanwarjag]

I am working on RNA binding protein in that context I extracted all mouse genes 3'UTR regions make a FASTq file and aligned my data with that FAstq file. However when I upload that file IGV cannot take it as well as Seqmonk also says gene names can not be recognized. What is the best way of viewing such file of 5'UTR regions in IGV. I would assume 5'UTR is already there in mouse gene in IGV but still it does not accept it.

The IGV error is

[BWA_on_data_1_and_data_10_A4].bam does not contain any sequence names which match the current genome.  File:      ENSMUST00000114660|0610007C21Rik|0|0|715, NM_001081394.1|0610007L01Rik|0|0|2468, ENSMUST00000159957|0610007P08Rik|0|0|1384, ENSMUST00000021676|0610007P14Rik|0|0|666, ... Genome: chr1, chr2, chr3, chr4, ...

Answer 1

[Sean Davis]

IGV is a genome viewer, so the only sequence names it recognizes are chromosome names. Your best bet is to align your data to the genome, not the 3'UTRs.