stringtie_expression_matrix

[gp519c]

Hello!

Thank you for providing so much help for RNAseq analysis.
I am fairly new to coding and all that involves. I am trying to use the stringite_experession_matrix script, but I cannot run it:

./stringtie_expression_matrix.pl --expression_metric=TPM --result_dirs='SD_WT_24_ballgown, SD_e3_24_ballgown' --transcript_matrix_file=transcript_tpm_all_samples.tsv --gene_matrix_file=gene_tpm_all_samples.tsv

Could not find specified result dir: SD_e3_24_ballgown

I think my problem is related to where the files are located. I cant find any documentation/explanation of --results_dirs.
Where should I run this? The names of results_dirs should correspond to my .gtf files generated with Stringtie?

Thank you very much!

[guo-cheng]

I also have similar problem. when I run this script, the log says could not find transcript id in line:
Any one met this problem?
The --results_dirs refers to stringtie main outputs, including the transcripts.gtf file.

[dionne099]

@guo-cheng I have also run into the same problem. This is what some of the lines looks like: Could not find transcript id in line: Htub.Chr1.H1 StringTie transcript 390434 393299 1000 - . gene_id "Htub.ptg003393l.g282"; transcript_id "Htub.ptg003393l.g282.t1"; cov "1.266447"; FPKM "0.107125"; TPM "0.137167";

Where you able to fix this problem?

[dionne099]

I was able to fix the problem with the suggestion here: griffithlab/rnaseq_tutorial#24

Thank you Griffith lab for your tools!