Closed huangwb8 closed 2 years ago
I also encountered the same problem
@htw1124 Maybe prepDE.py3
had been out of maintaining. Toolkits like featureCounts
works well in the calculation of read count. You could try.
Hi~ I also encountered the same problem and saw your problem, but I didn't find a good solution. However, after my attempt, I succeeded in running and got the results, but I don't know whether it is useful for you. You can refer to it. First of all, this is my error report:
Error: could not locate transcript mRNA:Solyc04g024965.1.1 entry for sample 2A
Traceback (most recent call last):
File "./prepDE.py", line 283, in <module>
geneDict[geneIDs[i]][s[0]]+=v[s[0]]
KeyError: '2A'
I use 2.2.0 Stringtie version. I found prepDE in the stringtie folder Python3 script, so I use Python3 to run prepDE.py3 this script and ran successfully. I hope this method will help you.
The issue was identified and fixed in v2.2.1 release https://github.com/gpertea/stringtie/releases/tag/v2.2.1
Hello! I am using v2.2.1 but encounter a similar error.
CH_RNA-ZF_BPATCS/CH/EC_output$ prepDE.py -i sequence_mapping.txt -g genematrix.csv -t transcriptmatrix.csv
Error: could not locate transcript gene-b0731 entry for sample Chl1-2
Traceback (most recent call last):
File "/home/ryan/stringtie/prepDE.py", line 284, in <module>
geneDict.setdefault(geneIDs[i],{}) #gene_id
KeyError: 'gene-b0731'
I tried to recheck and made sure that I had -e on all my generated files but still same error.
Hi~ I use stringtie v2.1.6 to calculate TPM of genes and transcripts, and it works well. However, when I came to
prepDE.py
orprepDE.py3
to prepare read count matrix for DESeq2 or edgeR, some error appeared.My stringtie code is like:
I set the
preDE.config.txt
:When I run
prepDE.py
orprepDE.py3
, like:The error appeared:
I found similar problems exist in other issues, but the bug seemed to be fixed in the new version of stringtie. Now I don't know how to deal with it.
Could you give some suggestions? Thanks!