xueyidong / longreadrna Goto Github PK

I was attempting to reproduce results for flames (NSC and sequins) analyses, but there are a couple of issues I would like to request help with.

1. gffcompare between my attempt to reproduce the flames NSC results and ./NSC/flames/results/isoform_annotated.filtered.gff3 are significantly different (ie Intron chain level: 62.4 (Sensitivity) | 36.5 (Precision) |). I noticed ./NSC/flames/config_bulk_nanopore.json file was last updated ~7 months ago but the ./NSC/flames/run_flames.sh file and the original gff3 results file were updated less than 1 month ago. Does this config file correspond to the posted results, as I would expect almost 100% agreement for sensitivity and precision? If not, could you please provide files that correspond to the results you posted in the paper?

2. Could you also please provide the config_sequin.json used for the flames sequins run?

Many Thanks!

I get the following error when attempting to reproduce run_flames.sh results for the sequins data

Command '['.../k8 .../paftools.js gff2bed .../sequins/annotations/rnasequin_annotation_2.4.gtf > \
.../tmp.splice_anno.bed12']' returned non-zero exit status 1

On further inspection, a manual attempt to convert the .gtf file, results in following error.

.../paftools.js:1593: ReferenceError: name is not defined
                        exons.push([t[0], t[3], t[4], t[6], id, type, name, tname]);
                                                 ^
ReferenceError: name is not defined
    at paf_gff2bed (.../paftools.js:1593:50)
    at main (.../paftools.js:2517:29)
    at .../paftools.js:2534:1

The .gtf seems not to be in proper format. Can you provide the properly formatted file?

Many thanks

Hello @XueyiDong,

Could you please quickly verify which counts are wild-type and gene-null in ./NSC/flames/results/pseudo_barcode_annotation.csv?

I presume
wild-type : barcode07 barcode{10..13}
gene-knockout : barcode{15..17}

Many thanks,
Akshay