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rcalandrelli committed Apr 16, 2019
1 parent 938991e commit 1d6fc1f19d72a48d5a25cade6468e88dc87e92cc
BIN +2 KB (120%) .DS_Store
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@@ -86,7 +86,7 @@ Now align the reads to the reference sequence:
where:

- ``-p`` refers to a specified number of parallel search threads (update it accordingly to your number of available cores). This can be useful to decrease the processing time in aligning the reads.
- ``-x`` specifies the basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final ``/.1.bt2``, ``/.2.bt2``, etc.
- ``-x`` specifies the basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final ``.1.bt2``, ``.2.bt2``, etc.
- ``-S`` specifies the output file in ``sam`` format.
- ```HiCfile1_log.txt``` and ```HiCfile2_log.txt``` are log files containing the statistics of the alignment:

@@ -25,8 +25,7 @@ The function ``run_hifive`` of [HiCtool_hifive.py](/scripts/HiCtool_hifive.py) i
```Python
execfile('HiCtool_hifive.py')
run_hifive(fend_file='restrictionsites_gc_map_valid.bed',
bam_file1='HiCfile_pair1.bam',
bam_file2='HiCfile_pair2.bam',
bam_file_1='HiCfile_pair1.bam', bam_file_2='HiCfile_pair2.bam',
restriction_enzyme='MboI',
model='Hi-Corrector')
```
@@ -27,7 +27,7 @@ The function ``run_hifive`` of [HiCtool_hifive.py](/scripts/HiCtool_hifive.py) i
```Python
execfile('HiCtool_hifive.py')
run_hifive(fend_file='restrictionsites_gc_map_valid.bed',
bam_file1='HiCfile_pair1.bam', bam_file2='HiCfile_pair2.bam',
bam_file_1='HiCfile_pair1.bam', bam_file_2='HiCfile_pair2.bam',
restriction_enzyme='MboI',
model='Yaffe-Tanay')
```
@@ -93,7 +93,7 @@ To calculate TAD coordinates for a chromosome (here for chr 6) use the function
execfile('HiCtool_TAD_analysis.py')
global_normalized_40kb = load_matrix_tab('output_ic_mes/output_normalized.txt')
tad_coord = compute_full_tad_analysis(global_normalized_40kb, a_chr='Y', isGlobal=True,
tad_coord = compute_full_tad_analysis(global_normalized_40kb, a_chr='6', isGlobal=True,
species='hg38', save_di=True, save_hmm=True)
```
``tad_coord`` is a list of topological domains. Each topological domain is a list of two elements that are the start and end coordinate of the domain. ``save_di`` and ``save_hmm`` set to ``True`` allow to save also the DI values and HMM biased states to txt file.

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