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Incomplete sashimi plots #106
Description
Dear all,
I am writing because I am having some issues in getting a complete sashimi plot starting from BAM files.
I can get the axes and the number or reads supporting the juctions but not the coverage along exons.
I report you the command line I used and attach the sample plots I get.
Can you please if something is missing in my command or what should I change. Moreover, I have a couple of additional questions.
Is it possible to the get an 'average plot' of groups of samples? If yes, how should it be specified in the input BAM list?
Moreover, how should the junction bed file look like? Is it meant as reference file or the coverage junction file per sample such as those produced by STAR for example? Can you please add some information? I could not find it on the github page.
Many thanks in advance.
Kind regards
Francesca
docker run --rm -v ${my_ref}:${my_ref} -v ${my_data}:${my_data}
guigolab/ggsashimi
-b ${my_data}/splicing/group_a.tsv
-c 12:5951843-6123196
-g ${my_ref}/Homo_sapiens.GRCh38.113.gtf
-o ${my_data}/splicing/sashimi_plot
--fix-y-scale
Activity
stale commentedon Oct 31, 2026
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.