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zhouyulab / igia

Integrative Gene Isoform Assembler
https://github.com/zhouyulab/igia
MIT License
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Some isoforms are filetered out #4

Open nlapalu opened 4 years ago

nlapalu commented 4 years ago

Hi,

I tried your pipeline with default parameters with long reads data (pacbio hq isoforms mapped with gmap) and NGS reads. A lot of my isoseq transcripts/isoforms (exons) were filtered out. See the attached file with an IGV screenshot. Firts track (bigwig of RNA-seq mapping with STAR), second track bam file of HQ isoseq mapped with gmap, third track gff of filtered isoforms, then IGIA results. There is no isoform for the PB.42 HQ isoseq isoforms, and the well RNA-seq supported isoform PB.43.3 is missing.

igia

Any ideas ?

nlapalu commented 4 years ago

Other thing, I get a lot of IsoF, but I didn't provide TSS or TES file. I expected a lot of IsoC.

sqreb commented 4 years ago

Could you provide the bam files of these two genes to help us fix this error. I would be grateful if you could send the test set to wangdehe@whu.edu.cn.

Hi,

I tried your pipeline with default parameters with long reads data (pacbio hq isoforms mapped with gmap) and NGS reads. A lot of my isoseq transcripts/isoforms (exons) were filtered out. See the attached file with an IGV screenshot. Firts track (bigwig of RNA-seq mapping with STAR), second track bam file of HQ isoseq mapped with gmap, third track gff of filtered isoforms, then IGIA results. There is no isoform for the PB.42 HQ isoseq isoforms, and the well RNA-seq supported isoform PB.43.3 is missing.

igia

Any ideas ?