Adding new Genomes to Flow

Flow App
1

Hi Flow team,

Could you add the “Arabidopsis thaliana” Genome to flow?

It’d be useful to be able to import or upload any new genome. Thanks.

Kind regards,
Paulo

2

Hi Paulo

We have added Arabidopsis thaliana to Flow - as you can see the RNA-Seq genome worked well: Flow

However there are some errors with preparing the genome for CLIP that will need to be resolved because the GTF file is non-standard containing no “biotype” tags for genes: Flow

If you have a working GTF file please do share it with us which will speed things up for you.

Best,
Charlotte

3

Hi Charlotte,

Thank you for adding this genome, and already trying to prepare it for CLIP.

I will do as suggested, to obtain a GTF file containing the “biotype” tag for genes.

Best,
Paulo

4

Hi Charlotte,

I’ve uploaded a GTF file for Arabidopsis, I can see it has “biotype” tag for genes.
Could you check if this file can be used to generate a genome for CLIP? Thank you.

Kind regards,
Paulo

5

Hi Paulo

Thanks for this!! It is better, but still causing an issue with iCount segment that I can’t figure out. Flow

The exact error is:

Executing the following command: iCount segment Arabidopsis_thaliana.TAIR10.59_bracketsremoved.cmd.gtf Arabidopsis_thaliana_seg.gtf Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.fai   
Input parameters for function 'get_segments' in iCount.genomes.segment   
    annotation: Arabidopsis_thaliana.TAIR10.59_bracketsremoved.cmd.gtf   
    segmentation: Arabidopsis_thaliana_seg.gtf   
    fai: Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.fai   
    report_progress: False   
[ValueError] need more than 1 value to unpack   
  File "/usr/local/lib/python3.9/site-packages/iCount/cli.py", line 448, in main   
    result_object = func(**args)   
   
  File "/usr/local/lib/python3.9/site-packages/iCount/genomes/segment.py", line 1015, in get_segments   
    for gene_content in _get_gene_content(annotation, chromosomes, report_progress):   
   
  File "/usr/local/lib/python3.9/site-packages/iCount/genomes/segment.py", line 906, in _get_gene_content   
    if interval.attrs['gene_id'] == current_gene:   
   
  File "pybedtools/cbedtools.pyx", line 392, in pybedtools.cbedtools.Interval.attrs.__get__   
   
  File "pybedtools/cbedtools.pyx", line 180, in pybedtools.cbedtools.Attributes.__init__

I checked and every GTF line has a gene_id and there are no lone gene_id’s that appear on only one line.

This will require some deeper investigation I’m afraid.

Best,
Charlotte

6

Hi Charlotte,

Thank you for the troubleshooting. I was wondering if you can try this GFF3 file instead?

Best,
Paulo