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