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shizhuoxing / scISA-Tools

single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single molecule resolution.
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Can not get flnc.tmap file #1

Closed RyanYip-Kat closed 3 years ago

RyanYip-Kat commented 4 years ago

When I run command: gffcompare -r ref.genes.gtf isoseq_flnc.Transcript.gff -o flnc I can not get the flnc.tmap And I also want to know what is your ref.gene.gtf

shizhuoxing commented 4 years ago

Hi，Ryan In generally, you can download the gene annotation gtf file specific for your own data on Ensembl, Genecode or NCBI for one species. For this repo I uploaded example CCS data, the species is the cynomolgus monkey, which is consistent with our preprint paper. May be when you set the right of “ref.gene.gtf” file for gffcompare you can get the flnc.tmap, by the way, gffcompare output the flnc.tmap file to the same path with you "isoseq_flnc.Transcript.gff".

RyanYip-Kat commented 4 years ago

But When I used the css.bam data you provided in the example_data ,and my genome is : Macaca_fascicularis.Macaca_fascicularis_5.0.dna.toplevel.fa,gtf file is Macaca_fascicularis.Macaca_fascicularis_5.0.100.gtf.I can not get the .h5 file with your pipeline scripts.And I always got the error when I used sqanti3_qc.py,the error like : *** Predicting ORF sequences... terminate called after throwing an instance of 'std::length_error' what(): basic_string::_S_create GeneMarkS: error on last system call, error code 134 Abort program!!! And the .isoform.matrix is NULL .And how can I fixed these issue ! Thanks!

pigraul commented 3 years ago

Hello, I ran into the same problem.

When I run command: gffcompare -r ref.genes.gtf isoseq_flnc.Transcript.gff -o flnc I got the following files: flnc.isoseq_flnc.Transcript.gff.tmap flnc.isoseq_flnc.Transcript.gff.refmap flnc.tracking flnc.annotated.gtf flnc.loci flnc.stats

Is the file "flnc.isoseq_flnc.Transcript.gff.tmap" same to the "flnc.tmap", or the "flnc.tmap" file was indeed not generated?

Thanks

shizhuoxing commented 3 years ago

@pigraul hi, "flnc.isoseq_flnc.Transcript.gff.tmap" same to the "flnc.tmap", i have modified this in this repo's README.