How to obtain gene length of yeast for tpm computation?

Question

[melatoninixo]

Hi all,

I am trying to get gene lengths of yeast to obtain tpm values. I have tried using gtftools but the output seemed to only be gene lengths on the X chromosome. I have tried the same command I ran using the yeast gtf file with the demo file given in the downloadable zipped folder but instead obtained the full output for it.

The below is the command I used:

python gtftools.py -l s288c_genelength.txt '/home/abir/Desktop/genome fasta and gtf files/Saccharomyces_cerevisiae.R64-1-1.105.gtf' 

Do I need to further specify anything? Any help is greatly appreciated, thank you!

[Pappu]

You can try biomart or ensembl rest api.

Answer 1

[GenoMax]

Using EntrezDirect. Redirect to a file and then find the gene length.

$ esearch -db gene -query "Saccharomyces cerevisiae [ORGN]" | efetch -format tabular | awk -F "\t" '{OFS="\t"}{print $6,$11,$13,$14}' -
Symbol  chromosome      start_position_on_the_genomic_accession end_position_on_the_genomic_accession
SUP35   IV      808324  810381
RAD52   XIII    212515  213930
RAD51   V       349980  351182
CYC1    X       526335  526664
ACT1    VI      53260   54696
CDC28   II      560078  560974
GCN4    V       138918  139763
RPO21   IV      205360  210561
SPT15   V       465303  466025

[melatoninixo]

Is it possible to specify the yeast strain?