velocyto-notebooks
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velocyto-team
Dear all, I'm studying the germline cells and I isolated single nuclei from single germ cells and sequenced the content with Illumina Hiseq paired-end platform. The Nuclei are huge and...
Hello, I already have a sorted bamfile and I am using the velocyto `run` command. Is there a way to skip the built-in sorting step other than renaming the input...
Hi, I am writing to seek your help with an issue I have with generating RNA velocity figures in R and python - the direction of the arrows don't seem...
Dear velocyto-team: I experience unable to read in the trial loom file showed as below, any suggestions? Thank you very much. The Error Messenge: >>> vlm = vcy.VelocytoLoom("/data/DentateGyrus.loom") Traceback (most...
Thanks for you excellent script. But when I run own data ,which have generate '.loom' file, I always face the traceback following. I notice that the sample you used have...
Dear velocyto team, The spliced and unspliced model is really excellent! I have been testing your method for three weeks, but can't produce good results. Our project is about the...
Hello, looking at the jupyter notebook code I had errors with both notebooks when calling the following line: vlm.set_clusters(vlm.ca["ClusterName"], cluter_colors_dict=colors_dict) changing "cluter_colors_dict" to "cluster_colors_dict" solved this issue. However, running through...
Hello, I would like to run velocyto on a time series of bulk RNA-seq. Each time point is 24 hours apart. I did the alignment with STAR and as it...
Dear, Can loom files be obtained only by the bam file after alignment? Can I get a loom file from the gene expression matrix which is easier to download?If there...
Hi, I have aligned bam files from different platforms (Smartseq2 and inDrop methods). Is it possible to run pyvelocyto on a population of cells coming from different platforms ? I...
