Error in prepDE.py in Tuxedo protocol after StringTie quantification
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3.2 years ago

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.

DESeq2 StringTie new Tuxedo protocol RNA-Seq • 2.2k views
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You can try another library in R called tximport.

https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html

The link above is a full tutorial how to import data to DESeq2. It also includes data from StringTie. Maybe it can solve your problem quicker.

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Thank you very much I'll do it

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You should change this ti an acutal answer :-)

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Can you share the contents of ./prepDE.py or a github link to the script.

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While you indeed cannot run DESeq2 this is not the cause of your error. Your error lies within the prepDE.py script from the Tuxedo pipeline. I have altered your title to better describe your problem.

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Thank you for your reply. I downloaded the script again and it ran successfully, The problem was in the script bymistakenly something would have got editted by me.