1/6/2024 0 Comments Free download Bartender 5![]() one on the forward read and one on the reverse read), we recommend concatenating the sequences to generate one longer UMI. The user can also refer the corresponding section (Bartender Extractor) for more details. There is an example script (./example/random_small_data/test_extractor_umi.sh) illustrating how to add umi paramter to the command line. Bartender has also provides an option to extract UMI and barcode in the same step. The user can replace this line number with the corresponding UMI in the original read file. In the extracted barcode file, the line number is associated with each extracted barcode and this will act as a default UMI for clustering without UMI handling (each barcode read has a unique line number and therefore a unique UMI). Bartender provides a way to assign a unique molecular identifier (UMI) to each barcode read to handle PCR jackpotting errors. Once the barcode is extracted, we can group similar extracted barcodes into putative barcodes by using the bartender clustering component (bartender_single_com). The Bartender clustering component will also accept a unique molecular identifier (UMI) instead of a line number in these files and this is discussed below. There is a bash script containing the actual command (/example/random_small_data/test_extractor.sh). It also reports the total number of reads, total number of reads that have valid barcode, and total number of reads that have valid reads that pass the average quality score to the command line. This command outputs the extracted barcode and the line number in input file to 2M_extracted_barcode.txt in the following format: The command to perform this is:īartender_extractor_com -f 2M_test.fq -o 2M_extracted -q ? -p TACCAAAATTATAA -m 2. We name the output file as 2M_extracted_barcode.txt by giving the prefix - 2M_extracted. Here we will filter out any read with average quality score less than 30 (corresponding ascii code is '?'). You can filter out low quality reads by specifying a lowest average quality score as an ascii value. In this example, we will allow one mismatch each at proceeding and suceeding sequences. Both proceeding and succeeding sequences have 4 characters. It has four random regions separated by 3 spacers. The barcode pattern in the 2M_tst.fq file is TACCAAAATTATAA. We first extract barcodes from an example fastq file (2M_tst.fq) using the bartender extraction component (bartender_extractor_com). The raw input is 2M_test.fq, a file containing 1000 reads (250 unique reads). The data is in example/random_small_data folder. Please download this project to your local machine in order to go through this example. ![]() The results also provide the quality of the discovered barcode in the position matrix format. This exmaple illustrates how to converte a raw fastq reads file to a frequency table containing discovered barcode and raw reads count. ![]() This section will introduce Bartender with a simple example. If you want to change the install directory, you need to make a small change to the Makefile. The default install directory is /usr/local/bin and is hard coded in the make file. To build three components in one batch: make all.To build bartender_combiner (multiple time point mode): make bartender_combiner.To build bartender_extractor (barcode extractor): make bartender_extractor.To build bartender_single (barcode clustering): make bartender_single.If the Bartender is run in Ubuntu operating system, please make sure the system version is 16.04 or above as the built-in GCC compiler in old Ubuntu operating system does not support regex very well, which might cause failures of bartender extractors. It generates count trajectories for time-course data.īartender uses a gcc compiler which should be no older than gcc47.It clusters barcode reads and counts the frequency of each cluster.It extracts barcodes from FASTA or FASTQ files. ![]() Bartender is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. Bartender is a c++ tool that is designed to process random barcode data. ![]()
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