Ka Ming Nip comments

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                                            Ka Ming Nip

RNA-Bloom Generates Empty FASTA Without Error

Thanks for reporting this! Yes, this happens when there are too few reads.

RNA-Bloom Generates Empty FASTA Without Error

I was able to replicate this, but this is not a bug. The assembled sequences are too short and they all end up in `rnabloom.transcripts.short.fa` (instead of `rnabloom.transcripts.fa`). I have...

RNA-Bloom Generates Empty FASTA Without Error

Not at all. The length threshold is the only determining factor for assigning sequences to these two files.

RNA-Bloom Generates Empty FASTA Without Error

There is already an option for that (i.e. `-length`) and its default value is 200, which is what separates the sequences in the two files. All RNA-seq assemblers I can...

RNA-Bloom Generates Empty FASTA Without Error

Sorry, I thought you were asking whether RNA-Bloom use any evidence to determine that threshold.

Coverage does not add up

The sum isn't the same because each base of a given read can be assigned to more than one contig, especially when it aligns to the overlap between two contigs....

Coverage does not add up

In the above diagram, contigs 1 and 2 can still be join together into a transcript if there is sufficient overlap at the contig edges. Double-counting can also happen when...

ERROR: For input string: "9223372036854775808"

Can you please print the first few lines of `rnabloom_k17.hist`? e.g. ``` head rnabloom_out/rnabloom_k17.hist ```

ERROR: For input string: "9223372036854775808"

This number `9223372036854775808` is just larger than the largest 64-bit long integer in Java, i.e. `9,223,372,036,854,775,807`. Can you please report your ntCard version? ``` ntcard --version ```

ERROR: For input string: "9223372036854775808"

This looks like a bug in ntCard. Can you share your read sequences with me?