Hi, I am using cluster_gff to cluster primary alignments of an ONT cDNA data and I notice that some exons which should be clustered together are missing in the output gff file of cluster_gff, for example:
The upper panel is the primary alignments before cluster_gff, and the lower panel is the output gff file of cluster_gff. Most reads shown in this screenshot are filtered out in the output cluster_memberships.tsv file. And I think there should be exons in the place where I marked with question mark.
Here are my commands:
spliced_bam2gff -s -t 20 -M only_primary.sort.bam > raw.gff
cluster_gff -p 1.0 -t 20 -c 2 -d 30 -e 30 -a cluster_memberships.tsv raw.gff > clustered_transcripts.gff
How could I finetune the parameters to prevent these reads from being filtered out? Could you give some advices?
Hi, I am using cluster_gff to cluster primary alignments of an ONT cDNA data and I notice that some exons which should be clustered together are missing in the output gff file of cluster_gff, for example:
The upper panel is the primary alignments before cluster_gff, and the lower panel is the output gff file of cluster_gff. Most reads shown in this screenshot are filtered out in the output cluster_memberships.tsv file. And I think there should be exons in the place where I marked with question mark.
Here are my commands: spliced_bam2gff -s -t 20 -M only_primary.sort.bam > raw.gff cluster_gff -p 1.0 -t 20 -c 2 -d 30 -e 30 -a cluster_memberships.tsv raw.gff > clustered_transcripts.gff
How could I finetune the parameters to prevent these reads from being filtered out? Could you give some advices?
Thanks.