Set isoform abundance cutoff to FLAIR quantify

[ulbivin]

Hi, I have a set of samples for which I am running FLAIR. Some samples have a unique isoform which make up a substantial fraction of the gene transcript from that specific sample, but only a small fraction of the combined isoforms from all samples. Hence it is filtered out when running FLAIR quantify.

Is there a way to set the filter for FLAIR quantify to include less abundant isoforms in the count.tsv file?

[Jeltje]

When I go to the flair/test directory and run flair quantify -r test_input/reads_manifest.txt -i test_input/test.collapse.isoforms.fa -o test_out/quant and then look at the first ten lines of test_out/quant.counts.tsv:

ids     A1_A_b0 A2_A_b0 A3_A_b0 B1_B_b0 B2_B_b0 B3_B_b0
ENST00000225792.10_ENSG00000108654.15   22.0    12.0    10.0    11.0    15.0    13.0
ENST00000256078.9_ENSG00000133703.12    7.0     6.0     7.0     15.0    11.0    7.0
ENST00000311936.8_ENSG00000133703.12    10.0    9.0     7.0     19.0    18.0    7.0
ENST00000348547.6_ENSG00000125991.19    38.0    36.0    46.0    66.0    47.0    46.0
ENST00000451605.1_ENSG00000125991.19    13.0    29.0    16.0    29.0    28.0    16.0
ENST00000557334.5_ENSG00000133703.12    3.0     0.0     4.0     8.0     10.0    4.0
HISEQ:1287:HKCG7BCX3:1:1101:14093:55880_ENSG00000133703.12      0.0     0.0     1.0     0.0     3.0     1.0

The last line has single read counts for two of the samples.

What is your command precisely, and which version of FLAIR are you running?