Hello, I am doing RNA-seq analysis, using the pipeline after StringTie quantification step, I have decided to use DESeq2 package(count-based methods) for Differential expression analysis DESeq2 and using the following commands:
python2.7 ./prepDE.py -i sample_list.txt
But every time I am facing an error
Traceback (most recent call last): File "./prepDE.py", line 274, in <module> my_writer.writerow(geneDict[i]) File "/usr/lib/python2.7/csv.py", line 152, in writerow return self.writer.writerow(self._dict_to_list(rowdict)) ValueError: I/O operation on closed file
Since I don't know python I couldn't be able to solve this issue.
my sample_list file contains:
Treatment1 ./path/to/.gtf/file/which/is/obtained/from/stringtie/reestimation Treatment2 ./path/to/.gtf/file/which/is/obtained/from/stringtie/reestimation Control1 ./path/to/.gtf/file/which/is/obtained/from/stringtie/reestimation
. . . and so on The output which i am getting is transcript_count_matrix.csv and gene_count_matrix.csv from which gene_count_matrix.csv doesn't contain any values except first row:gene_id and Treatment1, Treatment2, Control1,etc
Any help in this regard will be deeply appreciated.