How to find read count for a newly discovered transcript

Question

[c_u]

I recently came across a paper where the authors found a novel pseudogene (human). I don't think they mention the genomic location for it, but they did submit the RNA sequence for it in Genbank (they think its a lncRNA). I have RNA-seq data from some patients, and I want to check the levels of this (possible) lncRNA in those samples. Is there a way I can do it?

One solution could have been to look at the reads in IGV for this locus (after loading the bam file from the data), but I don't think the genomic location for this gene is provided in the paper. Is there another way?

[WouterDeCoster]

You can blat the sequence to get the genomic location, for example from the UCSC genome browser.

Answer 1

[lieven.sterck]

Yes, either map the transcript (lncRNA) to the genome (human?) to get the genomic coordinates of that new gene then overlay your aligned BAM file for read counts or add that transcript to the set of human transcriptome and then map your reads to that and do read counting

[c_u]

Thanks Lieven. I have a couple of questions about that. First, regarding mapping the transcript to the genome, wouldn't only the exonic regions be mapped, since the transcript may not have the intronic region? Secondly, I never knew about mapping reads to a transcriptome. Is there a popular software to do that? Thank you!

[GenoMax]

salmon for mapping reads using a transcriptome (https://salmon.readthedocs.io/en/latest/ ) .

[lieven.sterck]

yes, correctly but that is the only thing you need. If you have the exons then the introns are simply the regions between the exons. (== if you have mapped the exons you can deduct the whole gene-locus from it).

For tool suggestion I support genomax suggestion for Salmon.

[mks002]

For mapping you can use Hisat program and then you use Depth of coverage under GATK program . By this exactly u can know about the coverage for the particular transcripts. -L option u check while running the GATK program where you can provide your interest of transcript in bed format (so for particular transcript of your interest results will be generated).