This document describes the submission format for mapping the initial reads to the final transcript model,
This file is included in the experiment directory and must be named read_model_map.tsv.gz.
To better understand how each pipeline deals differently with the same initial input, it will be asked to the participants to submit a .tsv file that relates the starting point (the reads provided by LRGASP) to their final transcript models. This file will have two columns:
read_id It will contain the ID of the “raw” sequence, and must be present in the source BAM or FASTQ file.transcript_id It will show the transcript model’s ID built using the read in the previous column. The transcript ID must be as it is in the GTF or FASTA submitted by the participant.If a read is not used to generate any transcript model it may be omitted or have its transcript_id column specified as *.
Here the first column is the IDs of the reads in the FASTQ rep1 of ENCODE pilot data set. It is just an example, the relations between ccs read, and transcript models are “made up”.
read_id transcript_id
m54284U_191110_105540/6/ccs ENCODEHT000595433
m54284U_191110_105540/8/ccs ENST00000329251.4
m54284U_191110_105540/9/ccs ENST00000392222.6
m54284U_191110_105540/13/ccs ENCODEHT000420932
m54284U_191110_105540/18/ccs ENCODEHT000260030
m54284U_191110_105540/19/ccs ENST00000336023.9
m54284U_191110_105540/21/ccs ENST00000468812.5
m54284U_191110_105540/33/ccs ENST00000234590.10
m54284U_191110_105540/35/ccs ENST00000398598.7
m54284U_191110_105540/41/ccs ENST00000392246.6
m54284U_191110_105540/49/ccs ENST00000238561.9
m54284U_191110_105540/50/ccs ENST00000558083.2
m54284U_191110_105540/54/ccs ENST00000216146.8
m54284U_191110_105540/56/ccs ENST00000374479.3
m54284U_191110_105540/57/ccs ENST00000301821.10
m54284U_191110_105540/59/ccs *
m54284U_191110_105540/60/ccs ENST00000247655.3
There is no limitation about reporting one single read linked to several transcript models, and vice versa. However, it is still unclear how this might be evaluated (or even if it should be evaluated).