"The -c and -m parameters of StringTie are not effective.

[tongtongy666]

During the bam-gtf conversion step, I set the -c 3 parameter, but when I checked the generated gtf file, I found that there were still transcripts with cov values less than 3. I did not handle them and merged them together. The file size was about 140.2MB. Later, I found that the -m parameter was set to 50 by default during the merging process, so I changed it to 200. However, I found that the resulting gtf.tamp file still contained transcripts with a length less than 200, and I was confused as to why. I also tried adding the -c parameter again during the merge step, but it didn't work, and it still generated a file with the same size of 140.2MB as before. Can you explain this to me?"

stringtie --merge -m 200 -c 3 -F 1 -p 8 -G tringtie -p 8 -G update.gtf \ -o ZS/mappingputout/GTF/7121BSF.gtf \ --rf -c 3 -m 200 -l

[mpertea]

These parameters only apply to the novel transcripts assembled by StringTie, not to the ones in the reference, i.e. the ones in the file, provided with the -G parameter.

[tongtongy666]

These parameters only apply to the novel transcripts assembled by StringTie, not to the ones in the reference, i.e. the ones in the file, provided with the -G parameter.

Thank you，So, stringtie -- merge-c 3-m 200 should work, right? But the resulting new file, "mergenew.gtf," is the same size as the one I created without setting the -c 3 parameter。 And in this part “--merge “， -m parameter was set to 50 by default during the merge process, so it was changed to 200.However, I found that the generated gtf.tamp file still contained transcripts less than 200 in length。

[tongtongy666]

These parameters only apply to the novel transcripts assembled by StringTie, not to the ones in the reference, i.e. the ones in the file, provided with the -G parameter. Do you mean that these parameters set the new transcripts produced after assembly, and those less than 200 that are already present in the reference genome are still present? Or should I not provide the -G argument and just "merge "or "merge.list"？