Issue with finding matching exome/makeLinkedTxome

[malawsky]

Hello,

Thank you for making a fantastic rna seq analysis pipeline!

I ran Salmon using the following transcriptome:

ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz

Salmon ran perfectly fine on all my samples. However, I am trying to use tximeta to prepare the data for DESeq2 analysis yet when I run tximeta I get:

couldn't find matching transcriptome, returning un-ranged SummarizedExperiment

I tried using makeLinkedTxome but it gives me an error when trying to pass it my local salmon index directory:

Error: lexical error: invalid char in json text.
                                      /proj/gershont/projects/salmon/a
                    (right here) ------^

Thank you very much for your help!

Best, Danny

[mikelove]

Can you post your version? If you are using the latest or second latest version of Bioc it should work automatically. I.e. tximeta version 1.6.1 or 1.4.1.

(That should fix it, but also the other issue you posted involves updating jsonlite)

[malawsky]

I am running version tximeta_1.0.3. Do I need to update it then?

[mikelove]

In that 1.0 < 1.4, yes 😉

[malawsky]

it worked! thank you!