# Desperate! Salmon-quant to DESEQ2 gives me 0 lines? **URL:** \ **Category:** Uncategorized\ **Tags:** transcriptomics, deseq2, salmon\ **Created:** [March 15, 2023, 11:44am UTC](https://help.galaxyproject.org/t/desperate-salmon-quant-to-deseq2-gives-me-0-lines/9649 "2023-03-15T11:44:23Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![aabdesales812](https://avatars.discourse-cdn.com/v4/letter/a/e95f7d/32.png) [@aabdesales812](https://help.galaxyproject.org/u/aabdesales812)\ **Post date:** [March 15, 2023, 11:44am UTC](https://help.galaxyproject.org/t/desperate-salmon-quant-to-deseq2-gives-me-0-lines/9649/1 "2023-03-15T11:44:23Z")
Hello All, I am relatively new to this sort of analysis. I have paired-end reads from Oncopeltus tissue. I ran these under Salmon-quant to generate TPMs. I then used these as input files into the newest version of DESEQ2 using the gff3 annotation file from the oncopeltus genome. The program runs, but returns outputs with nothing in them. Please help! A ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 13, 2023, 11:35pm UTC](https://help.galaxyproject.org/t/desperate-salmon-quant-to-deseq2-gives-me-0-lines/9649/2 "2023-04-13T23:35:11Z")
There is much Q&A about these tools at this forum. Please review what has worked for others. Focus on the reference data first – both content and format – since a mismatch between identifiers is the most common root issue. I added a few tags to your topic that will find these, plus you can also just search with tool names, datatypes, error messages, etc to get started. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [July 22, 2025, 10:02pm UTC](https://help.galaxyproject.org/t/desperate-salmon-quant-to-deseq2-gives-me-0-lines/9649/3 "2025-07-22T22:02:33Z")