Download transcriptome.csv for tximport analysis

Question

[Morris_Chair]

Hello everyone,

I'm using tximport ( or trying to..) to import into R quant.sf information obtained with salmon. Tximport requires a human transcriptome.csv to use but I don't know from where I can download it,

I read that is better to download it directly rather then making it from a fasta format,

thank you in advance

[ATpoint]

This has been asked before. That post contains a possible solution using BiomaRt using tximport to prepare salmon quantification files for DEG analysis. Also been asked on Bioc.

[ATpoint]

Also a solution here How tximport work with gencode transcripts?

[Morris_Chair]

Hi ATpoint,thank you for the links, they gave me a direction how to proceed buy I still have issue... At the end seems that I can not download this file and I have to create it by myself.

The way I do is this

txdb <- makeTxDbFromGFF(file="~/RNAseq/annotation/genome/gencode.v19.annotation.gtf", format=("gtf"), , organism= "Homo sapiens")

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.


seqinfo(txdb)

Seqinfo object with 37 sequences (1 circular) from an unspecified genome; no seqlengths:
  seqnames   seqlengths isCircular genome
  chr1             <NA>       <NA>   <NA>
  chr2             <NA>       <NA>   <NA>
  chr3             <NA>       <NA>   <NA>
  chr4             <NA>       <NA>   <NA>
  chr5             <NA>       <NA>   <NA>
  ...               ...        ...    ...
  GL000212.1       <NA>       <NA>   <NA>
  GL000220.1       <NA>       <NA>   <NA>
  GL000228.1       <NA>       <NA>   <NA>
  GL000237.1       <NA>       <NA>   <NA>
  GL000241.1       <NA>       <NA>   <NA>

All the values are NA,\ I have tried also with different GFF files but the result doesn't change

this problem was shown also the in the link you gave to me but remain unsolved , Is there a specific package for you to create this file?(such as biomartr) , it has to be with two columns, one with gene ID and the other with trascripts

Thank you

[Kevin Blighe]

Why do you have an empty entry in your command? - you have 2 commas side by side.

Please update your version of Bioconductor

[Morris_Chair]

Hi Kevin,

The reason why something was missing between commas, is because I keep changing parameters and contents of command line and it happened by mistake to be empty when I posted here.

The version of bioconductor is this below and for some reason I can not make further update (I have limited right on the computer that I use). Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.0 (2018-04-23) I will split this discussion because the next question is like another thread