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griffithlab / rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
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stringtie_expression_matrix.pl #46

Open najibveto opened 2 years ago

najibveto commented 2 years ago

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: image

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 commented 7 months ago

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