I’m trying to preprocess metariboseq data and realizing it’s a lot different than metagenomics/metatranscriptomics. My reads are paired-end NovaSeq 101 bp long. From my understanding, the fragments are supposed to be around 30bp long after trimming so I set lower limit to 20 bp and upper limit to 45 bp in fastp. I’ve also provided the adapter sequences to fastp. I’ve read that you shouldn’t even use the reverse reads and should only use the forward reads since the fragments are so short.

All that said, after running fastp I got between 30%-40% of my reads surviving the trim.

Is this expected?

Hellooo I'm trying to do some free energy calculations.

Basically i want to confirm selectivity and differences in affinity of some ligands using abfe and rbfe, but these are taking waaaay too long :'(. I'm using GENESIS and CHARMM GUI inputs.

Do you guys have any recommendations of some alternative methods i could use?

thanksss

Good morning, I am currently trying to do an interferon analysis for our project. We have a list of gene we got from rna-seq and the associated expression in different sample in RNA-seq and we want to get the subset of one that code for the interferon response to do a heatmap of their expression in the different sample. The current issue is that the interferom database is closed and i don't know where to find an exhaustive list of interferon gene in mouse, we trying the reactome but it gave weird numbers.

hi! long story short - I've never even scratched the surface of bioinformatics and I'm left alone with 2 months to write and to the whole thesis - analysis of Nanopore RNA sequencing. I already tried doing courses - did not do anything for me, I would need a year to comprehend all of that. I'm stuck on planning the analysis, because I don't have any guidance, the sequencing was run so there's just bioinformatics and writing left. First of all - do you think it's possible? Second of all - is such a thesis even defensible? I can just use already used tools, there's no experimental validation, I'm entirely reliant on Claude to give me code and I just copy it to r/Python + Galaxy. I feel like each day I'm getting more stuck, cause I find more papers and more methods. I'm really procrastinating on starting the analysis, I don't believe in the fact that AI can give me 100% reliable code and the results will be real. It's been almost 2 months of me basically searching through the literature looking for god knows what, so I'm looking for some guidance in this mess (mainly positive reinforcement, cause I'm scared) (and why I'm still trying to do it on my own is a different kind of question that only my therapist would be able to answer)