Deseq2 output 0 lines

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Hello! I ran a DeSeq 2 with 6 Sam files that I changed to tabular format. 3 are treated three are untreated and all are paired. I have ran the tool multiple times and consulted the other comment section related to this question, however no matter what I do the tool runs successfully but does not produce any lines of information. The only factor I put in was treat vs untreat, I unselected titles/headers as when I ran it with it produced an error, and I ran for Generate plots for visualizing the analysis results , Output normalised counts. Do you have any tips on how to fix this error?

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Hi @Priya_Das
What do you mean by “Sam files changed to tabular format”? Have you generated count tables using featureCounts, htseq-count or a similar tool?
Consider using this tutorial as a guide. Maybe try other tools such as voom or edgeR.
If you share the history, I can have a look. To share the history, click at History options (thee bars icon at the top right corner of the history panel > Share or publish > Make history accessible > Copy the URL and paste it into the reply.

Kind regards,
Igor

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http://cancer-bmv50c3.osumc.edu:8080/u/das31/h/copy-of-unnamed-history

Here is the history. I originally had bam files but I used the bam to sam tool to covert them to sam. I then when into the edit, datatypes, and then changed the datatype to tabular. I have not generated count tables so this might be the issue. I will attempt to use the tutorial to do this. Thank you for your help!

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Hi @Priya_Das
Thank you for the explanation! You are correct, featureCounts expects counts, not reads. Follow this tutorial.
Kind regards,
Igor

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Hi @igor, thank you so much for your help! Due to the fact that I have bam files already uploaded instead of URLs which are mentioned at the beginning of the tutorial would I need to start at the mapping step?

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Hi @Priya_Das
Follow Reads to counts tutorial (the link is in my first reply) or check other tutorials in Transcriptomics section. The job settings may vary, for example, built-in models are available only for small number of popular genome assemblies. You need a gene annotation for the genome assembly used for read mapping.
Kind regards,
Igor