EduEyras
commented
3 years ago Hi,
Yes, SUPPA will work with any GTF, regardless of how you obtained it.
The question is whether you want to apply it to the reads directly or to the resulting transcripts after running some transcript reconstruction program.
You have several options:
PacBio reads --> map to the genome --> BAM --> pinfish to generate GTF --> SUPPA
PacBio reads --> map to the genome --> BAM --> FLAIR/StringTie2/Talon/SQANTI --> GTF --> SUPPA
and one we have done too:
PacBio reads --> RATTLE to generate a reference-free transcriptome --> map transcripts to the genome --> BAM to GTF with pinfish --> SUPPA
Important points:
In most cases, after mapping/processing reads mapped to the genome, the output is not clustered into genes and transcripts. You would need to use option --pool-genes with SUPPA:
python3 ~/bin/SUPPA-2.3/suppa.py generateEvents -i transcripts.gtf -o se_events -e SE -f ioe --pool-genes
This option will group transcripts into genes, so that they can be considered together for alternative splicing events.
Also, I think that pinfish generates GFF from BAM, but maybe not GTF. But a simple command can generate a GTF for your transcripts, e.g.
egrep -v gene_id transcripts.gff | egrep -v "#" | awk '{OFS="\t"; print $1,$2,$3,$4,$5,".","+",".",$9." "$10" gene_id "$10}' > transcripts.gtf
That would the file you can run with SUPPA and with the --pool-genes option
I hope this helps
best
Eduardo
On Wed, 24 Mar 2021 at 19:04, 朱庆权 @.***> wrote:
Does suppa2 apply to pacbio iso-seq ?
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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ
zhuqingquan5510
Does suppa2 apply to pacbio iso-seq ?