transcript read count from alignQC

[weihongqi]

Dear Jason,
May I ask how can I export read counts of all transcripts after running alignQC on a bam file? Which data file corresponds to all transcript read counts?

For example, for one report, all the files that can be dump are the following:
alignqc dump output_report.xhtml --list

alignment_error_plot.pdf
alignment_stats.txt
alignments.pdf
annot_lengths.pdf
annot_lengths.txt.gz [annot_lengths.txt]
annotbest.txt.gz [annotbest.txt]
best.sorted.bed.gz [best.sorted.bed best.sorted.gpd]
bias.pdf
bias_table.txt.gz [bias_table.txt]
chimera.bed.gz [chimera.bed chimera.gpd]
chrlens.txt
context_error_data.txt
context_plot.pdf
covgraph.pdf
depth.sorted.bed.gz [depth.sorted.bed]
error_data.txt
error_stats.txt
exon_size_distro.pdf
feature_depth.pdf
gapped.bed.gz [gapped.bed gapped.gpd]
gene_full_rarefraction.txt
gene_rarefraction.pdf
gene_rarefraction.txt
junvar.pdf
junvar.txt
lengths.txt.gz [lengths.txt]
pacbio.pdf
params.txt
perchrdepth.pdf
read_genomic_features.pdf
read_genomic_features.txt.gz [read_genomic_features.txt]
techinical_atypical_chimeras.bed.gz [techinical_atypical_chimeras.bed techinical_atypical_chimeras.gpd]
technical_chimeras.bed.gz [technical_chimeras.bed]
transcript_distro.pdf
transcript_full_rarefraction.txt
transcript_rarefraction
transcript_rarefraction.txt

Many thanks,

Weihong