Low number of isoforms detected

[jadedavis5]

Hi,

I am attempting to use FLAMES for isoform detection from Nanopore direct RNA data in barley. However, when running it with one sample BAM I am getting a very small isoforms gff of only 139 genes and isoforms. This is a stark contrast to the ~47k transcripts in the reference genome annotation I am using.

I am running it with:

bulk_long_pipeline.py
--gff3 RGT_Planet_v1.gtf
--genomefa RGT_Planet_1.fasta
--outdir RGT_output
--inbam rna_011_ptt_f32_control_RGT_Planet_1_aln_sorted.bam --config_file config_bulk.json

This is my configuration file (it is all default settings except for transcript quantification being changed to false as I also encountered the same problem as issue #44) :
{
"comment":"config",
"pipeline_parameters":{
"do_genome_alignment":true,
"do_isoform_identification":true,
"do_read_realignment":true,
"do_transcript_quantification":false
},
"global_parameters":{
"generate_raw_isoform":false,
"has_UMI":true
},
"isoform_parameters":{
"MAX_DIST":10,
"MAX_TS_DIST":120,
"MAX_SPLICE_MATCH_DIST":10,
"min_fl_exon_len":40,
"Max_site_per_splice":3,
"Min_sup_cnt":5,
"Min_cnt_pct":0.001,
"Min_sup_pct":0.2,
"strand_specific":-1,
"remove_incomp_reads":4
},
"alignment_parameters":{
"use_junctions":true,
"no_flank":false
},
"realign_parameters":{
"use_annotation":true
},
"transcript_counting":{
"min_tr_coverage":0.4,
"min_read_coverage":0.4
}
}