stringtie_expression_matrix.pl

[najibveto]

hello,
thank you for the rnaseq tutorial.
i was trying to use the script "stringtie_expression_matrix.pl" to Extract FPKM/TPM or coverage results and i used the following code:
perl stringtie_expression_matrix.pl --expression_metric=FPKM \ --result_dirs='alevin_RNA-1,alevin_RNA-2,alevin_RNA-3,egg_RNA-1,egg_RNA-2,egg_RNA-3,FF_RNA-1,FF_RNA-2,FF_RNA-3' \ --transcript_matrix_file=transcript_tpms_all_samples.tsv \ --gene_matrix_file=gene_tpms_all_samples.tsv
for the files of transcripts gtf, their structure is as follow:

when i run the command, i got the following error:
Processing data for the following 9 samples:
Could not find transcript id in line: 1 StringTie transcript 135071 135516 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; cov "6681.424805"; FPKM "1365.562866"; TPM "3094.511230";
how is possible the fix the problem?
thank you for your help.

[liu1441452945]

Hello, I have the same problem as you. Have you found a solution now?@najibveto