pavanvidem
commented
1 year ago Hi, Thanks for using ChiRA! I highly recommend you to use the latest version of ChiRA. It has algorithmic improvements and some bug fixes over previous versions.
You can get GTF and transcriptome FASTA files from Ensembl FTP. If you are using miRNA interactome data, you can get miRNA GTF and FASTA files from miRBase. In that case, please remove any miRNA sequnces and annotations that are also present in Ensembl annotations. Make sure that you have a compatible genome FASTA file too (chromosome IDs must match). FASTA files also available on Ensembl.
I reproduced this tutorial on command line and everything worked flawlessly with the latest version.
From the error message that you posted, it is possible that your BAM files are empty. Did your BWA mapping finished successfully? Can you please check whether index*.bam in the output directory are empty?
Best, Pavan
Hi Pavankumar,
Thank you for this program, it is nice to have a user friendly program available for completing analyses on RNA-RNA interaction datasets. So far there have been very few programs produced for this function.
I ran into 2 issues while running it:
First, I have been unable to find a GFF file that is correctly formatted that works on the chira_merge.py step. The 'whole_transcriptome.gff' file you provided with your tutorial works for mouse, but is there a repository I can download this file from for human?
Second, the chira_map.py step seems to run into issues in the newer releases of ChiRA (v1.4.3). From a fresh install using 'conda install -c bioconda chira', an error occurs that prevents completion of the step: [16-12-2022 17:19:11] START: Write alignments to BED [E::idx_find_and_load] Could not retrieve index file for 'outdirect/sorted.bam' This error does not occur with an earlier version of ChiRA I tried (ChiRA v1.0.2).
Please let me know if you can help with these issue.
Thanks for your help! Brandon