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CITE-seq-Count (version 1.4.4+galaxy0)

Input Type:

RNA-Seq FASTQ file, Barcode reads:

RNA-Seq FASTQ file, HTO/CMO reads:

the CMO/HTO barcodes as well as their respective names:

first column is the sequence and second column is the name

Configure Chemistry Options:

How many errors are allowed between two cell barcodes to collapse them onto one cell.:

How many errors are allowed between two umi within the same cell and TAG to collapse.:

Deactivate UMI correction:

How many cells you expect in your run:

Whitelist of cell barcodes:

Maximum Levenshtein distance allowed for CMO/HTO.:

How many bases should be trimmed on CMO/HTO read before starting to map:

Activate sliding window alignement.:

Output in tsv format (in addition to the dense format):

Select N reads to run on instead of all.:

Write table of unknown TAGs to file.:

CITE-seq-Count is a program that outputs UMI and read counts from raw fastq CITE-seq or hashing data.

Here is an image explaining the expected structure of read1 and read2 from the sequencer: