velocyto.py
velocyto.py copied to clipboard
velocyto-team
RNA velocity estimation in Python
when I run velocyto like this: >```r >velocyto run -b /home/shijian/scvelo1/ESCA-5-post-T_.tsv -m /home/shijian/scvelo/human_rmsk.gtf /WFDATA/yang_res_z/0901cp/ESCA-5-post-T/outs/possorted_genome_bam.bam /home/shijian/scvelo/genes.gtf -o /WFDATA/yang_scvelo/ESCA-5-post-T > and I got error as follow: > ```r >Traceback (most recent call...
Hello, Thank you for creating such an innovative tool! I am using `velocyto` upstream of `scvelo` to analyze my 10x single cell sample and am encountering some strange results. `scvelo`...
Hi, I'm new to python and I met a problem during installation. Can anyone give me some advice? Maybe I should try to install pysam first? ``` /xtdisk/miniconda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible...
Hi, I have been trying to run velocyto run10x, but I keep getting this error for my sample folder: Error: Invalid value for 'SAMPLEFOLDER': Directory '~rds/.../filtered_feature_bc_matrix' does not exist. Could...
Is there anyone who has run into this particular error message when running velocity estimations using velocity.R? If so, please advise on how to proceed. I'm running my analysis on...
Hi velocyto team, I have a quick question regarding the pre-velocyto process using cell ranger. The new Cell Ranger 5.0 has a new "**include-introns**" option for counting intronic reads. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview...
Hi, I try to run velocyto on inDrops data. I preprocessed row data with inDrops pipeline (github.com/indrops/indrops) and I obtain a bam file like this: AGCGTGGT-GCTTTGGC:TAGTGC:NB501677_71_HJCH5BGX2_2_23101_13130_2406 16 1 4491139 255...
Hello, I have 10x data that I have initially analyzed using cell ranger and scanpy and I was now starting the analysis with velocyto. I have performed counting on cellranger...
Hi, When I run the velocyto to convert the bam file to loom file. I met error as: no BGZF EOF marker; file may be truncated. Is it means the...
Hi guys, I'm running velocyto on bam files via ssh. One sample was succeeded, but when I started running the other two samples, I saw this error showed up over...
