Some errors in construction of annotation file (consExons.gtf/Introns.gtf)

[BoomSophie]

Hello, I had some trouble to construct the annotation files for exon and intron.
I've installed the updated annotation files in Ensembl (Homo_sapiens.GRCh38.104.chr.gtf). I've tried to run the step1, the result size of the constructed annotation files for exon and intron are only about 10M per file. Also the final results are invalid, which showed all reads for exon and intron were 0.
However, I succeed to obtain the reads for exon when I replaced the constructed annotation file for exon(consExons.gtf) as the original file( (Homo_sapiens.GRCh38.104.chr.gtf))
I'll appreciate it if you can reply to me.

[hsnajafabadi]

Hi. There is a new branch that is still not merged with the master branch: https://github.com/rached-97/CRIES. It contains an R script to generate constitutive exons and intronic regions. Could you please see if this update solves the problem?

[BoomSophie]

Hi. There is a new branch that is still not merged with the master branch: https://github.com/rached-97/CRIES. It contains an R script to generate constitutive exons and intronic regions. Could you please see if this update solves the problem?

Hi.I got new trouble when I tried to export the file (Homo_sapiens.GRCh38.104.gtf_constExonsAndIntrons_Ensembl.gtf)

I got the following error:
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'Homo_sapiens.GRCh38.104.gtf_constExonsAndIntrons_Ensembl.gtf': Permission denied'

Could you please tell me how to solve the problem?

[rached-97]

Hi @BoomSophie ,

generate_const_intronsExons_gtf.R by default writes its output to the same directory as the input gtf. You appear to not have permissions to write to that directory. I have added another argument to the R script to allow you to specify the output directory. Let me know if that solves your problem.

Rscript generate_const_intronsExons_gtf.R <path_to_input_ensembl_gtf> <desired_output_syle_[Ensembl or UCSC]> <output_directory>

[BoomSophie]

Hi @BoomSophie ,

generate_const_intronsExons_gtf.R by default writes its output to the same directory as the input gtf. You appear to not have permissions to write to that directory. I have added another argument to the R script to allow you to specify the output directory. Let me know if that solves your problem.

Rscript generate_const_intronsExons_gtf.R <path_to_input_ensembl_gtf> <desired_output_syle_[Ensembl or UCSC]> <output_directory>

Hi. I've succeed in running this program under your help. I'm appreciate for your help!

[LXsasse]

Hi, I was wondering which method would be the correct one to use to get the gtf file, the bash script under step 1. or the R script? I was able to generate gtf files with both scripts but when I used them on my bam files they resulted in different counts for introns. The log2-counts between both methods are correlated with 0.9 but still not a perfect match. On the other hand, exon counts are the same for 99.9% of genes.