Maxim Karpov

Hi, what do the columns in the coords and cnv files represent? The files were produced without headers.

> > > > I do not get header INFO, either. In my thought, they may: ref_chr ref_start ref_end query_chr query_start query_end ref_copy query_copy. I do not know about the...

> Hi, did you manage to fix this? You can try adding "row.names=NULL" argument to "alignments = read.table(opt$input_filename, stringsAsFactors = F, fill = T)" in the script file.

> Hello @Maxim-Karpov, > > Thank you for your interest in `finder`. We are currently working on developing a different version of `finder` that will address most of the issues...

@RacheliHadjez @WietseHR It is possible to tweak the code to run STARlong which is a modified version of STAR designed for aligning long reads, however, its performance in this use...

@lefterov This issue could be due to the formatting of your metadata file or your reads. Have your paired-end(?) reads been split beforehand? e.g. from reads.fastq to reads_1.fastq + reads_2.fastq...

Upon further research, it seems that, due to the long intron length, gffread (having an intrinsic intron length limit of 6Mb) splits these exons into two separate entries. The emergence...

I wrote a script to concatenate the duplicate sequences inside the combined_split_transcripts_with_bad_SJ_redundancy_removed.fasta file. I was able to resolve the gffread issue by rebuilding the singularity container in sandbox mode and...