Stringtie --merge and gtf_list.txt issue

Question

[Morris_Chair]

Hello guys,

I’m having problems merging the GTF files generated with Stringtie. I know it must me a simple mistake that I m doing with the cmdline but also googling I couldn’t figure it out.

The command line that I’m using for merging the files is this:

stringtie --merge -G Homo_sapiens.GRCh37.75.gtf -p 8 -o Treated_1.gtf Treated_2.gtf Treated_3.gtf Untreated_1.gtf Untreated_2.gtf Untreated_3.gtf gtf_list.txt

Error: no transcripts were found in input file gtf_list.txt

Beside the error that , it generates a folder with files inside named “Transcript_s000.bam and sam” but I can’t understand why it stops working.

In the file "gtf_list.txt' I listed the file name_gtf

Can you please help me with that?

Thank you

[lakhujanivijay]

Paste the contents of gtf_list.txt

your contents should look like this

assembly/ERR188044_chrX.gtf
assembly/ERR188104_chrX.gtf
assembly/ERR188234_chrX.gtf
assembly/ERR188245_chrX.gtf
assembly/ERR188257_chrX.gtf
assembly/ERR188273_chrX.gtf
assembly/ERR188337_chrX.gtf
assembly/ERR188383_chrX.gtf
assembly/ERR188401_chrX.gtf
assembly/ERR188428_chrX.gtf
assembly/ERR188454_chrX.gtf
assembly/ERR204916_chrX.gtf

[Morris_Chair]

Hi bioExplorer,

here is the head of my gtf.txt file which is different than yours, did you put also the path beside of each? in my case the txt file is in the same folder of the gtf files so I think I should be ok

[@ws7910 Files.GTF]$ head gtf_list.txt
Treated_1.gtf
Treated_2.gtf
Treated_3.gtf
Untreated_1.gtf
Untreated_2.gtf
Untreated_3.gtf[@ws7910 Files.GTF]$

This gtf come out from this command line,

stringtie file.bam -o file.bam.To.gtf -G Homo_sapiens.GRCh37.75.gtf --rf -A Treated_1.txt

Thank you

[lakhujanivijay]

Can you provide the absolute paths in the gtf_list.txt like this?

for e.g. say your gtf files are in /home/user/assembly directory, then your gtf_list.txt should look like

/home/user/assembly/ERR188428_chrX.gtf
/home/user/assembly/ERR188454_chrX.gtf
/home/user/assembly/ERR204916_chrX.gtf

AND, I noticed that your command is incorrect, it should be

stringtie --merge -G Homo_sapiens.GRCh37.75.gtf -p 8 -o stringtie_merged.gtf gtf_list.txt

stringtie --mergegenerated single output file called stringtie_merged.gtf.

[Morris_Chair]

Hole' ! problem solved , I have this precious file !

Basically I had to specify the path into the txt file

Thank you

PS: my previous command line was used to generate every single file.txt from single BAM files