RNAseq single-end FASTQ files - No data?

[EmilyB]

Hi,

I tried processing single-end FASTQ files (with Japanese Quail Reference - Kallisto) but I don’t get any data…

I’m not sure if I’m doing something wrong, as I’ve never processed single-end files before. I was using a dataset that’s already on ExpressAnalyst (under Reference → USGS Study 4). Please find attached the images of my workflow.

Any help would be greatly appreciated.

[EmilyB]

Hi again,

I was wondering if anyone is able to answer my question above…

Thank you,
Emily.

[Guangyan]

Dear Emily,

I am looking into the issue now. I will update you when it’s solved.

Thanks,
Guangyan

[Guangyan]

Hello Emily,

I consulted with Peng and it seems like for single ended RNA-seq data you need to specify these two values for single-ended data: Fragment length and SD of fragment length. We tried with 350 and 50 respectively and we are able to get the results.

Guangyan

[EmilyB]

Hi Guangyan,

Thank you for getting back to me. Can you please explain why the SD of the fragment length is 350?

[Guangyan]

We tried 350 after reading this post on BioStar: https://www.biostars.org/p/9543067/

Regards,
Guangyan

[EmilyB]

Ok!

I read the post, but just to clarify the parameters should as followed:

fragment length = 350
SD = 50

Not the other way around, correct?

Thanks,
Emily.

[Guangyan]

Yes, this is correct