cufflinks FPKM values

Question

[Nobody]

Hello community. I am using Cufflinks for transcript modeling however the result gives me zero FPKM values for genes that are expressed . someone had the same problem? do you have an interpretation for that

Answer 1

[Kevin Blighe]

Dear Zac, if the expression value is 0, then it likely implies that no reads aligned / mapped to that gene, further implying that it is not expressed in the samples at which you are looking.

If you feel that there is a potential other explanation, then please elaborate a bit further.

Cordiali saluti,

Kevin

[Nobody]

I looked on IGV to see if we really have mapping in these regions, indeed we have them

[Kevin Blighe]

Can you please, then, highlight the output file(s) in which you are seeing zero values.

[dsull]

1. Google: cufflinks zero fpkm -- there seem to be many reasons why FPKMs might be zero.
2. Cufflinks isn't really actively maintained anymore and is hardly ever used nowadays (indeed, the senior author of the software considers it to be "Retired Software"). For read mapping+counting, there are better tools. For assembly, there are also better tools.

[Nobody]

Could you please show me where the main author said this? Could you show me what assembly tools exist nowadays ?

[dsull]

Yes, it's on his website: https://pachterlab.github.io/software.html

Assembly tools include stringTie and Trinity.