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I've been trying to follow the instructions for preparing my data after running Rail-RNA and am having problems with the amount of dependencies these additional tools need and getting them to run. Some do not look to be maintained.

Release of a docker container would greatly assist this if it is possible.

To whom, it may concern.
I would like to run the same pipeline used to generate Recount2 in my dataset.
To check if the rail-RNA pipe worked correctly I ran it on a small project uploaded in Recount2 (SRP047399)

Rail-RNA was run using this command:
rail-rna go local -x dir_bowtie_hg38 dir_bowtie2_hg38 -m manifest_file --log dir_log_file -d tsv,bw,jx -f --scratch temp_folder_dir

based on Bowtie and Bowtie2 indexes for the reference genome hg38. Downloaded from:

I genome Illumina:

• ftp://ussd-ftp-illumina.com/Homo_sapiens/UCSC/hg38/Homo_sapiens/sequences/BowtieIndex
• ftp://ussd-ftp-illumina.com/Homo_sapiens/UCSC/hg38/Homo_sapiens/sequences/Bowtie2Index

I used the following data to run the R scripts after the rail-RNA pipeline.

• https://github.com/leekgroup/recount-website/raw/master/genes/Gencode-v.25.bed
• https://github.com/leekgroup/recount-website/raw/master/genes/counts_groups.Rdata
• https://github.com/leekgroup/recount-website/tree/master/rse/introns_unique.Rdata
• https://github.com/nellore/runs/raw/master/gtex/hg38.sizes

However when I match the gene counts or exon counts that I obtained against those uploaded in Recount2 I found some differences. In some cases, these differences resulted in more than 100.000 read counts

Moreover, I get this error when I run the prep_merge.R script
oo <- findOverlaps(jx_gr, introns_unique, type = 'equal')
stopifnot(length(unique(queryHits(oo))) == length(oo))

Can this be due to the use of wrong annotations?

I read that the tool is deterministic, I expected to obtain the same results. I check the number of reads in input and they are the same. However, the number of mapped reads is different

Do you have any idea why this happens?
Considering that I would like to compare my samples with the data in Recount. Please, can you confirm that the pipeline and the reference and the annotation files are correct?

Thank you.
Best Regards,
Gianluca

Please find below an example for one of the sample.