Geo Pertea

high-level workflow example

1

Thank you for this excellent work - I have been looking for something like this for a while as I often needed to explore transcript assemblies within a gene or...

I realize this involves some complex design/implementation changes and it is a feature more suitable for a full genome browser which is not the goal of this package. For cases...

extend `to_diff()` to junctions

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The `to_diff()` function is great for showing differences between exons, but sometimes it is very useful to highlight differences between introns and individual splice sites. Not sure if it wouldn't...

"Total Reads" misleading, how to get the input read count?

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Using release version 2.4.2 I've been using rnaseqc for a while on aligment files where I kept secondary alignments and also the unmapped reads. I naively assumed that "Total Reads"...

Currently only the basic exon structure and some basic GTF tags are preserved when gffcompare is running in "annotation mode", where a single input transcript file is given (+ a...

add option to assemble transfrags in the combined.gtf output

1

A new option (e.g. `--assemble`) should allow gffcompare to extend the transfrag-merging ability in the resulting `combined.gtf` output. Intron-compatible transfrags could be merged based on at least _n_>=1 matching introns,...

The '.' class code shown in the .tracking and .combined.gtf files for multiple input files is a result of the transcripts merged there across multiple samples having different relationships (class...

Currently the output is as follows: `>transcriptID CDS=value feature1=value;feature1=value;` However, this is problematic for parsing since `space` is used to separate CDS whereas `semicolon` is used to separate the other...

_Originally posted by @Maarten-vd-Sande in https://github.com/gpertea/gffread/issues/21#issuecomment-777736924_ > Just dropping in to say that supporting multiple tables would be an awesome feature (for me). I haven't found any other tool that...