search

FemeniasM / ExplorATEproject

R package to explore active transposable elements with RNA-seq data
17 stars 3 forks source link

error salmon quant: cannot recognize file extension #7

Closed silulinlulu closed 5 months ago

silulinlulu commented 11 months ago

Hello

I am using ExplorATE to quantify TE expression in my data and ecountered the following error: Quantifying with Salmon =======================ESC(BESC[m ESC[31m[2023-10-13 11:58:53][ERROR] FileExtensionError: Invalid extensionESC(BESC[m ESC[32mSupported extensions are: <.fq> or <.fastq> or <.fq.gz> or <.fastq.gz>ESC(BESC[m

i don't know why this occurs because the read files are all named as read1.fq.gz, which shold be the format that salmon can recognize. to prove this, i ran salmon quant seperately using the reference files generated by ExplorATE before the error, on the same read files and it worked fine.

could you please shed a light on this issue?

Thank you very much and i am looking forward to your reply.

Silu

BravoScarleth commented 5 months ago

Hi silu,

Maybe the response is too late for you to solve the problem. But it can be useful to others. I had the same problem and I fixed it easily. Literally, the names of the input PE sequence files must have _R1 and _R2. Example: sample_R1.fq and sample_R2.fq. In your case it should be called read_R1.fq.gz and not read1.fq.gz.

Regards

silulinlulu commented 5 months ago

Hi

Thanks very much for the reply. I realized this was the problem after I posted the issue. Thanks anyways.

Regards Silu