Counts for specific transcripts are missing

[JonLJ]

Hi!
I am trying to use RNASkim. It seems to be quite fast and easy to use.
However, I am worried about two things:

1. When I took the final list of expression, I wanted to look at the expression of some specific transcripts... however, these transcripts were not quantified. I do not the reason... could be that these transcripts are too short? I think that they are not that short. Is it a complicated region? I do not know.

Nonetheless, when I use other aligners (tophat, bowtie+bitseq) , I can see perfectly the expression of these transcripts. Why is RNASkim failing? For the rest of transcripts, it seems to work properly.

Any suggestions?
Example of transcripts that are not quantified are:
ENST00000408968
ENST00000526612
ENST00000399808
ENST00000602429
among others...

2. I have my fastq file compressed (fastq.gz). And it is quite slow uncompressing the files, and then run the ./rs_count command,... is there any way to use fastq.gz files? Like opening on the fly?

Many thanks!!!!
Jon