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stringtie Error: input file cannot be found

Hello,

I want to use StringTie to assemble transcripts for each sample, but when I run the stringtie, I have an error:

Error: input file –l cannot be found!

here is my command: 

stringtie -p 8 -G /annotation/Ghirsutum_458_v1.1.gene.gff3.gz -o NMHT-80-23.gtf –l NMHT-80-23 NMHT-80-23.bam

Please kindly let me know what should I do?

rna-seq rna-seq alignment sequence assembly
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updated by spriyar • spriyar • written by mjavad2012 • mjavad2012

Have you tried giving a different name for your output transcripts for the -l option?

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written by GenoMax GenoMax

yes, I did but i still have that error. what format supposed to be the output file after -l ?

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written by mjavad2012 • mjavad2012

For POC, try eliminating the -l, and let it use the default STRG. You can do a sed later, sed -i 's/STRG/NMHT-80-23/g' NMHT-80-23.gtf if it works.

The user manual also as the bam file in front of the options:

stringtie <aligned_reads.bam> [options]*
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written by st.ph.n st.ph.n

2 answers

This error may be due to strings error in the script options. I do suffer the same problem while i copied the script directly from article and paste it into terminal. (*Name of output perfix –l =error (which i copied from article); -l = working)

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written by Ellango R • Ellango R

That's right. As Pertea pointed, in the paper code we can found '–' instead of '-'; the first one is a character not recognized by stringtie. The problem is fixed just using the small '-'.

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written by jpuntomarcos • jpuntomarcos

Have you tried using the full path for the reference files. I had the same problem and adding the path to the genome reference solved it! Good luck!

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written by spriyar • spriyar

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