RNA-seq files not found (GSM id listed)

[luli-9885]

To whom this may concern,

I am trying to extract counts from some RNA-seq samples (listed below). They are from dataset GSE109125. I have tried extracting them from the new ARCHS4 browser and from the human_gene_v2.5.h5, with little sucess.

GSM2932603 T.4.Nve.Sp#1_RNA-seq
GSM2932604 T.4.Nve.Sp#2_RNA-seq
GSM2932609 T.8.Nve.Sp#1_RNA-seq
GSM2932610 T.8.Nve.Sp#2_RNA-seq

In the process, we think samples GSE2932488 to GSM2932646 are all not processed.
Feel free to contact me if there are any instructions I could try.

Thank you and best,
Lu

[diamantido]

Good morning Lu,

Thank you for using ARCHS4! I had a chance to look for the samples you provided, and it looks like our pipeline discovered them but encountered an issue while performing alignment. As a solution, I'd suggest using the archs4py package to align just these samples via their SRA run accessions (see example). Alternatively, we can run this alignment for you and share the results if you prefer. Let me know if you need any assistance!

Best,
Ido

[luli-9885]

Hi Ido,

I would like to see the results of your alignment. Also, I appreciate the instructions for the archs4py package!

I realized I made a mistake in my post regarding the samples being human. To clarify, I have tried mouse_gene_v2.5.h5 and human_gene_v2.5.h5. I am guessing the results from these samples wouldn't be available in mouse_gene_v2.5.h5; if they are in future updates of the H5 file, that would be wonderful.

Thank you for the prompt response! Happy Friday!

Best,
Lu