Question: Making genome-wide transcription level track from transcript level count
gravatar for Sam
16 months ago by
Sam10 wrote:

I used Salmon to quantify RNA at the transcript level. Is there a way to map this data into a format that can be viewed in IGV?

A related question, i also tried another method of quantifying where i aligned the read with STAR and counted with GenomicAlignments. The counts from this method is easily double that of the count from Salmon. With some transcripts counted almost 8x to 10x more. I did a Pearson's correlation and it return as value of 0.95, so i'm guessing it would not significantly affect me if i am doing genome wide analysis. But i am still curious as to how this discrepancy came about.

Any input will be greatly appreciated


rna-seq next-gen assembly • 249 views
ADD COMMENTlink modified 16 months ago by caggtaagtat1.4k • written 16 months ago by Sam10
gravatar for caggtaagtat
16 months ago by
caggtaagtat1.4k wrote:


I don't know about how to convert the data from salmon. I read, that you can generate pseudobam files with kalisto and maybe there is an tool for the output of salmon.

Concerning the STAR coverages, you get more reads, because it also counts gapped reads, which are not part of an already annotated transcript. Therefore, with salmon, where you only mapp the reads against annotated transcripts of a gene, you get a lot more reads, which also include splicing errors or not yet described alternative spicing events, where a gap can not be explained by already annotated transcript sequences. Salmon takes gapped reads into acoount, but only those who can be mapped to known transcripts. With gapped reads I mean gapped after alignment to the genome (like after STAR alignment). Thats why salmon an co are called pseudoalingers. They are fast and sufficient for well-annotated organisms. But you can't for example find new isoforms of a transcript.

ADD COMMENTlink written 16 months ago by caggtaagtat1.4k

I see, thank you very much for the explanation, it is very helpful!

ADD REPLYlink written 16 months ago by Sam10
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