Ka Ming Nip

1. RNA-Bloom doesn't generate GTF files. 2. You don't need to merge or concatenate read files for `-long`, `-ser`, and `-sef`. You can specify multiple file paths separated by space....

There could be much better ways to do this, but here is what I did in the past. For each tissue: 1. Align the assembled transcripts against the reference genome...

I don't understand what is a "complete BAM"? RNA-Bloom is primarily a reference-free assembly tool. It does not generate any BAM files against any reference. Regarding too many input files,...

Hi @sagnikbanerjee15 , I haven't used Trinity's genome-guided strategy. It would definitely help reduce total runtime and peak memory usage if the input reads were partitioned based on alignments against...

Hi @patrickaoude , For short-read RNA-seq data, I had often used fastp for trimming adapters, low quality bases, etc. RNA-Bloom's error correction for short reads is very similar to Rcorrector....

> * fastp documentation states that it actually is compatible with long reads from pacbio/ONT, I thought this may be useful for your knowledge. I have seen that message in...

The first two stages look fine. In stage 3, the overlapping step with minimap2 had some issues. The PAF output from minimap2 looks to be truncated. There should be 12...

I think your machine did not have enough memory to overlap the reads with minimap2 in stage 3. Also, I don't think PacBio Hifi reads are strand-specific. So, you shouldn't...

> Exception in thread "main" java.lang.OutOfMemoryError: Unable to allocate 20153865520 bytes Your machine does not have enough memory to do the assembly. The previous assembly ran further with a smaller...

For the first error, you forgot to specify an integer for number of threads. So, `-t THREADS` got errored out. I believed that you sorted out. For the 2nd error,...