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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
.TH UMIS "1" "April 2019" "umis 1.0.3" "User Commands"
.SH NAME
umis \- tools for processing UMI RNA-tag data
.SH SYNOPSIS
.B umis
[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]...
.SH OPTIONS
.TP
\fB\-\-help\fR
Show this message and exit.
.SS "Commands:"
.TP
add_uid
Adds UID:[samplebc cellbc umi] to readname for...
.TP
bamtag
Convert a BAM/SAM with fastqtransformed read names
to...
.TP
cb_filter
Filters reads with non\-matching barcodes Expects...
.TP
cb_histogram
Counts the number of reads for each cellular barcode...
.TP
demultiplex_cells
Demultiplex a fastqtransformed FASTQ file into a...
.TP
demultiplex_samples
Demultiplex a fastqtransformed FASTQ file into a...
.TP
fastqtransform
Transform input reads to the tagcounts compatible...
.TP
fasttagcount
Count up evidence for tagged molecules, this...
.TP
kallisto
Convert fastqtransformed file to output format...
.TP
mb_filter
Filters umis with non\-ACGT bases Expects formatted...
.TP
sb_filter
Filters reads with non\-matching sample barcodes...
.TP
sparse
Convert a CSV file to a sparse matrix with rows and...
.TP
subset_bamfile
Subset a SAM/BAM file, keeping only alignments from...
.TP
tagcount
Count up evidence for tagged molecules
.TP
umi_histogram
Counts the number of reads for each UMI Expects...
.IP
version
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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