# Question on conducting waafle\_junctions.py by single-end read

**URL:** <https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946>\
**Category:** WAAFLE\
**Created:** [December 27, 2021, 4:45pm UTC](https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946 "2021-12-27T16:45:20Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Xinming\_Xu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/xinming_xu/32/1164_2.png) [@Xinming\_Xu](https://forum.biobakery.org/u/Xinming_Xu)\
**Post date:** [December 27, 2021, 4:45pm UTC](https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946/1 "2021-12-27T16:45:20Z")

</div>

Hi there! I have a question for what if using single-end read when conducting waafle\_junctions step. Since the program need paired-ends reads or SAM file. Thank you in advance~

Xinming

---

<div class="post-metadata">

**Author:** ![microbemarsh](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/microbemarsh/32/2447_2.png) [@microbemarsh](https://forum.biobakery.org/u/microbemarsh)\
**Post date:** [October 2, 2023, 3:58pm UTC](https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946/2 "2023-10-02T15:58:17Z")

</div>

Same question here, would be helpful with long read sequencing data.

---

<div class="post-metadata">

**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [October 5, 2023, 4:30pm UTC](https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946/3 "2023-10-05T16:30:07Z")

</div>

Sorry to have missed the original question here. We don’t currently have a way to run the QC pipeline in WAAFLE within single-end reads. The pipeline was developed with the assumption that end-pairing would be informative for QC, although it would be possible to adapt the pipeline to work without this information. I’ll make a note about this for the future.

If you’re providing long reads as input to WAAFLE (in lieu of contigs) then you wouldn’t even need to perform this step, as its primary purpose is to weed out misassembly events.

---

<div class="post-metadata">

**Author:** ![microbemarsh](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/microbemarsh/32/2447_2.png) [@microbemarsh](https://forum.biobakery.org/u/microbemarsh)\
**Post date:** [October 11, 2023, 3:00am UTC](https://forum.biobakery.org/t/question-on-conducting-waafle-junctions-py-by-single-end-read/2946/4 "2023-10-11T03:00:20Z")

</div>

Great 🙂 thanks very much for all the wonderful tools you guys create and maintain!