hello
I use stringtie v2.2.3 to obtain counts data of transcriptome for downstream difference analysis.
This is my stringtie Code:
stringtie -p 8 -o "$spath/$id.gtf" -l $id -G $gtf -B -e $file
Then I provided a directory containing all sample subdirectories:
./sample1/sample1.gtf
./sample2/sample2.gtf
./sample3/sample3.gtf
At last, I downloaded the prepde.py3 version to get my counts information.
The code I use is as follows:
python3 $prepDE -i $output_dir -g "$output_dir/gene_count_matrix.csv" -t "$output_dir/transcript_count_matrix.csv" -l 133 -p "^A1" -v
Then the problem arises:
Error: could not locate transcript NM_011283 entry for sample A125
I found that other people also have this problem. According to those suggestions, I have checked my stringtie running log, and my stringtie runs without errors. And my scripts use the latest version. Now I don't know how to solve it.
Could you give some suggestions? Thanks!
hello I use stringtie v2.2.3 to obtain counts data of transcriptome for downstream difference analysis. This is my stringtie Code:
stringtie -p 8 -o "$spath/$id.gtf" -l $id -G $gtf -B -e $fileThen I provided a directory containing all sample subdirectories: ./sample1/sample1.gtf ./sample2/sample2.gtf ./sample3/sample3.gtf At last, I downloaded the prepde.py3 version to get my counts information. The code I use is as follows:python3 $prepDE -i $output_dir -g "$output_dir/gene_count_matrix.csv" -t "$output_dir/transcript_count_matrix.csv" -l 133 -p "^A1" -vThen the problem arises:Error: could not locate transcript NM_011283 entry for sample A125I found that other people also have this problem. According to those suggestions, I have checked my stringtie running log, and my stringtie runs without errors. And my scripts use the latest version. Now I don't know how to solve it. Could you give some suggestions? Thanks!