featureCounts- "An error occured with this data set"

I mapped my RNA seq data on mm10 genome using Bowtie2. Now that I want to count the reads by featureCount, it can not run it and i get the “An error occurred with this data set”. I tried it for my different samples but still i get the same error. Does anyone know what to do?


Hi @Mojtaba_Hoseini
I thought bowtie2 does not support spliced data, but I might be wrong. HiSAT2 is commonly used for species with spliced genes. Consider using this tutorial as a guide. It uses collections, but similar approach can be used with datasets.
Examine log files from the failed job and check error messages at the end. Click at any output from the failed job, click at ( i ) info icon and examine the standard output and the standard error log files in the middle window.
Hope that helps.

Kind regards,

Sure, thank you very much for advice. Highly appreciated.