You will know how to use w4CSeq by following this tutorial.
Provide your email address, so that you can receive the result link when a submitted job is completed.
Provide raw 4C FASTQ data. .gz format is accepted (and recommended for faster uploading). In addition, hard wired uploading is highly recommended for faster uploading.
Choose the reference genome build you want to use for alignment.
Choose the restriction enzyme you used for chromatin fragmentation. Choose primary enzyme if you take two rounds fragmentation strategy.
Suppose chromatin is fragmented with HindIII, your bait primer ATCTGCTATTGAGGAAGCTT should contain a HindIII cutting site AAGCTT at end. Then you should input the DNA sequence ATCTGCTATTGAGGAAGCTT. The analysis cannot be performed if you input it wrong, such as ATCTGCTATTGAGG or AAGCTTATCTGCTATTGAGG.
Provide the chromosome that inverse primers target , e.g. chr17
Provide the start position of inverse primer-targeting enzyme-digested chromatin fragment, e.g. 35497036
Provide the end position of inverse primer-targeting enzyme-digested chromatin fragment, e.g. 35504156
In this scenario, you should input:
"ATCTGCTATTGAGGAAGCTT" as DNA sequence of 4C target region
"35497036" as Start position of inverse primer
"35504156" as End position of inverse primer
Provide genomic bin size (number of enzyme sites) for statistical analysis of inter-chromosomal interactions; the default is 500
Provide genomic bin size (number of enzyme sites) for statistical analysis of inter-chromosomal interactions; the default is 100
Provide genomic window size (number of enzyme sites) for statistical analysis of intra-chromosomal interactions; the default is 3000
Provide your email address, so that you can receive the result link when a submitted job is completed.
Provide raw 4C FASTQ data; two FASTQ files from paired-end sequencing are needed. .gz format is accepted (and recommended for faster uploading). In addition, hard wired uploading is highly recommended for faster uploading.
Choose the reference genome build you want to use for alignment.
Provide the chromosome that inverse primers target , e.g. chr17
Provide the the REVERSE targeted positions of inverse primer 3'end on Bait Chromosome, e.g. 35504676
Provide the the FORWARD targeted positions of inverse primer 3'end on Bait Chromosome, e.g. 35504824
Provide the extended length(bp) from the primer position for alignment purpose (default 500bp)
In this scenario, you should input:
"35504676" as Start position of inverse primer
"35504824" as End position of inverse primer
Extension (default: 500bp) from the locations of the F1 and R1 primers are defined as bait for alignment.
Provide genomic bin size(bp) for statistical analysis of inter-chromosomal interactions; the default is 2000000
Provide genomic bin size(bp) for statistical analysis of intra-chromosomal interactions; the default is 400000
Provide genomic window size(bp) for statistical analysis of intra-chromosomal interactions; the default is 12000000