chmod +x ./bin/install.sh
./bin/install.sh
source env/bin/activate
chr1 982867 987410 chr1 1371055 1372952 1 313 363 984501 1372412 dm0 chr1 984316 984335 + 185 chr1 1372224 1372243 - 188
chr1 2194592 2197930 chr1 2378563 2382994 1 602 316 2195215 2381889 dm1 chr1 2195348 2195367 + 133 chr1 2381915 2381934 - 26
chr1 3452263 3454407 chr1 3618470 3620776 1 529 715 3453278 3619242 dm2 chr1 3453290 3453309 + 12 chr1 3619183 3619202 - 59
Every line is independent from each other. We will only do one line at a time. Each line will be conducted in only 1 second.
Column 1 and 2 (0-indexed) indicate the range of left anchor (left reference) and Column 4 and 5 indicate the right anchor.
We will need right anchor even when we do left anchor because we only want to rank GEMs that meet the left anchor and also with the rightmost fragment that is less than the right anchor region.
chr10 101762606 101763188 2 SHG8033-100000080-AAACACCAGAGGGTAABX8033-HEA-5-2-sub-1-1 E
chr10 104102286 104102852 2 SHG8033-100000080-AAACACCAGAGGGTAABX8033-HEA-5-2-sub-1-1 E
chr10 88838102 88838730 2 SHG8033-100000171-AAACACCAGCGCCCTABX8033-HEA-4-0-sub-1-1 P
Every line represents a fragment. Column 1 (0-indexed) represents the left point and Column 2 represents the right point of the fragment.
Column 3 (0-indexed), in this case 2, indicates the number of fragments in one GEM/chromatin complex.
Each GEM has a unique id (Column 4), so you can see that line 1 and 2 have the same Column 4 since they are the two fragments in the same GEM.
Ignore the 6th column.
Shield:
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