Run CamoTSS

CamoTSS includes two kind of modes : TC mode and CTSS mode.

The input files include:

alignment file (bam file)
annotation file (gtf file)
cell list file and reference genome file (fasta file)
cell barcode list file (csv file)

The output files include:

cell by all TSSs matrix (h5ad)
cell by two TSSs matrix (h5ad)
cell by CTSS matrix (h5ad)
cell by CTSS matrix (h5ad)
ref file (reference gene and TSS csv)

Here is a quick test file. You can check it.

Download test file

You can download test file from onedrive.

Here, you can download some large file include genome.fa, possorted_genome_bam_filtered.bam.

Alternatively, you can also download the reference genome fasta file from Ensembl or Genecode or website of 10x Genomics.

Run CamoTSS

Here are two modes in CamoTSS : TC and CTSS.

You can run CamoTSS by using test file according to the following code.

#!/bin/bash
gtfFile= $CamoTSS/test/Homo_sapiens.GRCh38.105.chr_test.gtf
fastaFile = $download/genome.fa
bamFile= $download/possorted_genome_bam_filtered.bam
cellbarcodeFile=$CamoTSS/test/cellbarcode_to_CamoTSS

CamoTSS --gtf gtfFile --refFasta fastaFile --bam bamFile -c cellbarcodeFile -o CamoTSS_out --mode TC

Options

There are more parameters for setting (CamoTSS -h always give the version you are using):

Usage: CamoTSS [options]

Options:
     -h, --help            show this help message and exit
     -g GTF_FILE, --gtf=GTF_FILE
                     The annotation gtf file for your analysing species.
     -c CDRFILE, --cellbarcodeFile=CDRFILE
                     The file include cell barcode which users want to keep
                     in the downstream analysis.
     -b BAM_FILE, --bam=BAM_FILE
                     The bam file of aligned from Cellranger or other
                     single cell aligned software.
     -o OUT_DIR, --outdir=OUT_DIR
                     The directory for output [default : $bam_file]
     -r REFFASTA, --refFasta=REFFASTA
                     The directory for reference genome fasta file
     -m MODE, --mode=MODE  You can select run by finding novel TSS cluster mode
                     [TC]. If you also want to detect CTSS within one
                     cluster, you can use [CTSS] mode

Optional arguments:
     --minCount=MINCOUNT
                     Minimum UMI counts for TC in all cells [default: 50]
     -p NPROC, --nproc=NPROC
                     Number of subprocesses [default: 4]
     --maxReadCount=MAXREADCOUNT
                     For each gene, the maxmium read count kept for
                     clustering [default: 10000]
     --clusterDistance=CLUSTERDISTANCE
                     The minimum distance between two cluster transcription
                     start site [default: 300]
     --InnerDistance=INNERDISTANCE
                     The resolution of each cluster [default: 100]
     --windowSize=WINDOWSIZE
                     The width of sliding window [default: 15]
     --minCTSSCount=MINCTSSCOUNT
                     The minimum UMI counts for each CTSS [default: 100]
     --minFC=MINFC       The minimum fold change for filtering CTSS [default:
                     6]