Shu Zhang

Dear deepTools group, Thanks for your wonderful tool. I used deeptools 3.5.1 and Python 3.9.12. When I was running computeMatrix for ATAC-seq peaks using code: computeMatrix reference-point \ -S ESC_ATAC.bw...

Bam file does not contain cell and umi barcodes appropriatelly formatted (Run on modified Smart-seq2 protocol)

9

Dear Velocyto Team, Our lab used a modified Smart-seq2 protocol to allow for multiplexed single-cell RNA-seq. Primers of RT reaction were designed with cell-specific barcodes and unique molecular identifier [UMI]....

Few arrows or chaotic arrows. What are the key parameters when analyze loom files?

1

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...

Error in "rdo.mapCor.gcCor = rd.gcCorrect(rdo.mapCor)"

1

Hi~ When I run "rdo.mapCor.gcCor = rd.gcCorrect(rdo.mapCor)", I got the error "Error in { : task 1 failed - "non-numeric argument to binary operator". I downloaded hg19 annotations from https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/readDepth/index.html....