niradsp

Reducing the number of CPUs being used

4

Hello, I just noticed that for some reason Bonito used up all of the 192 CPUs that my server has. Can this parameter be controlled somehow, or am I wrong...

Does the Bam file need to be sorted or unsorted?

9

Hello, So for example the EM algorithm used by rsem requires unsorted tramscriptome BAM file. Does Bambu have any such requirement? Also, I have 8 nanopore files, all compressed, sorted...

I have close to 21 samples and all of them are giving me a segmentation error message. I ran one of them in -v mode, and here is what I...

The mix option takes as input short-read data and long-read data. However, in my case, I have both PacBio and Nanopore data. The mix option does not allow 3 inputs....

I have previously been using FLAIR for the so-called "hybrid" method. That program allows short-read data to correct long-read data. I wanted to test stringtie's new --mix method. Here is...

I have some RIP-Seq data. If I want to do the analysis at the isoform level, will I be able to do that using clam? So for example, BAM file...

fetching sequence failed error message when running pileup

8

Here is my procedure. First I ran dorado basecaller, where I required all modifications to be called: ` dorado basecaller -v sup,inosine_m6A,pseU,m5C --min-qscore 9 --emit-moves -b 64 --mm2-opts {params} --estimate-poly-a...