Andre Sim
Andre Sim
Hi, It does look like there are a lot of reads in this region so I am surprised only two would be classified as full length. Is it possible to...
Hi, be on the look out for the next release of bambu as we have added partial matches to the trackReads output. See the documentation in the github readme for...
Hi there, Sorry for the extremely late response to your query. You are correct that these reads clearly look like they belong to Apex1-203 reads instead of Apex1-201. We currently...
Hi, Bambu should treat novel intron retention transcripts like any other so long as as intron retention doesn't result in a single exon transcript, there are some niche exceptions. In...
Hi, 1. Existence of an annotation missing the last exon Ok just to clarify to make sure I understand what is going on here, what method are you using to...
Hi there, did you have any success trying the above?
Hi both, Lets start with 2. first. So that I can understand the issue let me confirm some details, this issue only happens for some of your bam files, and...
Regarding the first question, I assume the link you posted is the SG-nex preprint (unfortuantely BioRxiv is down at the moment so I couldn't check). You can find the description...
Hi Sefi, Thanks for sharing this. This output is concerning as it says there are no reads for any of the annotated junctions which should not occur normally for a...
Hi Sefi, This all looks good, this definitely is narrowing down where the issue may be occurring. Do you happen to remember how many reads were listed for the samples...