--fusion_dist option in collapse module

[Drosofriends]

Hi, I tried to run collapse module on one single sample with the option --fusion_dist and this error occured:

Annotated ends extracted from GTF Read data extracted Single-exon genes grouped, collapsing Renaming isoforms using gtf Aligning reads to first-pass isoform reference A valid isoforms bed file needs to be specified: Failed at counting step for isoform read support

If I run the collapse module on one single sample without the option --fusion_dist everything works Any help? thank you!

[Jeltje]

Did you give it an isoform bed file?

Please include the full command you used when you create a ticket.

[Drosofriends]

python /home/Documents/FLAIR/flair-master/flair.py collapse --genome /home/Documents/gtf_genome/Dmel6.32.dna.toplevel.fa --reads /home/Documents/Fastq_files/Sample.fastq --query /home/Documents/FLAIR/flair_collapse/Sample_single_output/Sample.isoforms.bed --gtf /home/Documents/gtf_genome/Dmel6.32.106.gtf --threads 8 --support 3 --fusion_dist 10 --temp_dir /home/Documents/Elements/ --output /home/Documents/FLAIR/flair_collapse/Sample_single_output/sample

I tried to run this code once using the isoforms.bed generated by the collapse module and once using the corrected.bed in --query but the same error occured. What kind of .bed file I have to use?

[Jeltje]

Thank you! You did indeed find a bug.

Please replace your flair.py with the current version.

Reopen this ticket if this did not fix the problem.

[Drosofriends]

python /home/Documents/FLAIR/flair-master/flair.py collapse --genome /home/Documents/gtf_genome/Dmel6.32.dna.toplevel.fa --reads /home/Documents/Fastq_files/Sample.fastq --query /home/Documents/FLAIR/flair_collapse/Sample_single_output/Sample.isoforms.bed --gtf /home/Documents/gtf_genome/Dmel6.32.106.gtf --threads 8 --support 3 --fusion_dist 10 --temp_dir /home/Documents/Elements/ --output /home/Documents/FLAIR/flair_collapse/Sample_single_output/sample

  File "/home/Documents/FLAIR/flair-master/flair.py", line 49
    sys.stderr.write(f'Check that read file {rfile} exists\n')
                                                            ^
SyntaxError: invalid syntax

Hi I tried to run your  corrected flair.py but this error occured. Why?
thank you for your support

[Jeltje]

I can't repeat this problem. That section of the code did not change and it's from an unrelated part of the program (flar align instead of flair collapse). How did you download the code?

[Drosofriends]

I downloaded again the folder "flair-master" (with your corrected flair.py) and I replaced the old version flair-master with the new corrected one.

[Drosofriends]

I solved the problem by downloading the new version of FLAIR 1.7.0 and everything works well. Just another question, does fusion_dist option identify gene fusions in my sample? I run the collapse with this option(i.e. --fusion_dist 10) but I obtained only isoforms.bed isoforms.gtf and isoforms.fa where is the information about fusion_dist? Thank you a lot for fixing the bugs!!! :)

[Jeltje]

Fusion_dist was implemented to deal with reads derived from fusion genes. When such reads are aligned to a regular genome they tend to split between their genes of origin, and this was a way to be able to count them. We plan to remove this option in a future release as it's not really useful and creates confusion.