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94 changes: 48 additions & 46 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,11 +1,22 @@
INSTALLATION
==============


```
git clone https://github.com/vezzi/FRC_align/
cd FRC_align
```

You may need to install `cmake`, e.g. `sudo apt install cmake`

From the FRCurve directory run:
- mkdir build
- cd build
- cmake ..
- make

```
mkdir build
cd build
cmake ..
make
```

You will find the binaries in the main directory under bin. In case of problems the majority of the times there is a problem
with the local installation of boost.
Expand All @@ -21,68 +32,59 @@ applied in several de novo .

FRCbam
--------------
**USAGE: basic, no CE-stats tuning**

1. Assemble your data (n PE libraries and m MP libraries) with your favorite tools. Let us call the assemblies A_tool1, A_tool2, etc.
2. Align one PE library and one MP library against each of your assemblies (e.g., A_tool1)
1. Use the same parameters
2. PE library is mandatory, MP library is highly recommended
3. sort and index the generated bam files by coordinate. We will call them A_tool1_PE_lib.bam and A_tool1_MP_lib.bam
4. use PE library with largest read coverage (i.e., vertical coverage) and MP with largest spanning coverage (i.e., horizontal coverage)
3.Run FRCurve for each assembly:
```FRC --pe-sam A_tool1_PE_lib.bam --pe-min-insert MIN_PE_INS --pe-max-insert MAX_PE_INS -mp-sam A_tool1_MP_lib.bam --mp-min-insert MIN_MP_INS --mp-max-insert MAX_MP_INS
--genome-size ESTIMATED_GENOME_SIZE --output OUTPUT_HEADER```

where:

* ```--pe-sam``` A_tool1_PE_lib.bam```: sorted bam file obtained aligning PE library against assembly obtained with tool A;
* ```--pe-min-insert MIN_PE_INS```: estimated min insert length
* ```--pe-max-insert MAX_PE_INS``` : estimated max insert length
* ```--mp-sam A_tool1_MP_lib.bam```: sorted bam file obtained aligning MP library against assembly obtained with tool A;
* ```--mp-min-insert MIN_MP_INS``` : estimated min insert length
* ```--mp-max-insert MAX_MP_INS``` : estimated max insert length
* ```--genome-size ESTIMATED_GENOME_SIZE```: estimated genome size;
* ```--output OUTPUT_HEADER```: output header;

### USAGE: basic, no CE-stats tuning**

* `--pe-sam` A_tool1_PE_lib.bam`: sorted bam file obtained aligning PE library against assembly obtained with tool A;
* `--pe-min-insert MIN_PE_INS`: estimated min insert length
* `--pe-max-insert MAX_PE_INS` : estimated max insert length
* `--mp-sam A_tool1_MP_lib.bam`: sorted bam file obtained aligning MP library against assembly obtained with tool A;
* `--mp-min-insert MIN_MP_INS` : estimated min insert length
* `--mp-max-insert MAX_MP_INS` : estimated max insert length
* `--genome-size ESTIMATED_GENOME_SIZE`: estimated genome size;
* `--output OUTPUT_HEADER`: output header;

**IMPORTANT**:
If ```--genome-size``` is not specified the assembly length is used to compute FRCurve. In order to be able to compare FRCurves
obtained with different tools (and hence producing slightly different assembly sizes) the same ```ESTIMATED_GENOME_SIZE```
#### IMPORTANT:

If `--genome-size` is not specified the assembly length is used to compute FRCurve. In order to be able to compare FRCurves
obtained with different tools (and hence producing slightly different assembly sizes) the same `ESTIMATED_GENOME_SIZE`
must be specified.

OUTPUT:

* ```OUTPUT_HEADER_Features.txt```: human readable description of features: contig start end feature_type
* ```OUTPUT_HEADER_FRC.txt```: FRCurve computed with all the features (to be plotted)
* ```OUTPUT_HEADER_FEATURE.txt```: FRCurve for the corresponding feature
* ```OUTPUT_HEADER_featureType.txt```: for each featureType the specific FRCurve
* ```Features.gff```: features description in GFF format (for visualization)
* ```OUTPUT_HEADER_CEstats_PE.txt```: CEvalues distribution (for CE_stats tuning)
* ```OUTPUT_HEADER_CEstats_MP.txt```: CEvalues distribution (for CE_stats tuning)
#### OUTPUT:

* `OUTPUT_HEADER_Features.txt`: human readable description of features: contig start end feature_type
* `OUTPUT_HEADER_FRC.txt`: FRCurve computed with all the features (to be plotted)
* `OUTPUT_HEADER_FEATURE.txt`: FRCurve for the corresponding feature
* `OUTPUT_HEADER_featureType.txt`: for each featureType the specific FRCurve
* `Features.gff`: features description in GFF format (for visualization)
* `OUTPUT_HEADER_CEstats_PE.txt`: CEvalues distribution (for CE_stats tuning)
* `OUTPUT_HEADER_CEstats_MP.txt`: CEvalues distribution (for CE_stats tuning)

**USAGE: advanced, CE-stats tuning**
### USAGE: advanced, CE-stats tuning

CE-stats are able to identify the presence of insertion and deletion events. Different insert sizes give the possibility to
identify different events. In order to avoid too many False Positives (or too many False Negatives) a tuning phase is
highly recommended.

Once step 3 of USAGE is done, the user can already plot the FRCurves (for all the features or for only some of them).
CE_stats based features have been computed with default (i.e., not optimal) parameters. Each run of FRCbam produces two
files: ```OUTPUT_HEADER_CEstats_PE.txt``` and ```OUTPUT_HEADER_CEstats_MP.txt```. These files contain the distribution of the ```CE_values```
files: `OUTPUT_HEADER_CEstats_PE.txt` and `OUTPUT_HEADER_CEstats_MP.txt`. These files contain the distribution of the `CE_values`
on each assembly. These values must be plotted as suggested in page 3 of Supplementary Material
(see http://www.nada.kth.se/~vezzi/publications/supplementary.pdf) to estimate the optimal ```CE_min``` and ```CE_max``` values for
(see http://www.nada.kth.se/~vezzi/publications/supplementary.pdf) to estimate the optimal `CE_min` and `CE_max` values for
the PE and MP library respectively.
Once the optimal parameters are estimated FRCurves must be recomputed for all assemblies (only ```COMPR``` and ```STRECH``` features
Once the optimal parameters are estimated FRCurves must be recomputed for all assemblies (only `COMPR` and `STRECH` features
will change) specifying the following extra parameters:

* ```--CEstats-PE-min CE_PE_MIN```: all position with CE values computed with PE library lower than this are considered compressions
* ```--CEstats-PE-max CE_PE_MAX```: all position with CE values computed with PE library higher than this are considered expansions
* ```--CEstats-MP-min CE_MP_MIN```: all position with CE values computed with MP library lower than this are considered compressions
* ```--CEstats-MP-max CE_MP_MAX```: all position with CE values computed with MP library higher than this are considered expansions
* `--CEstats-PE-min CE_PE_MIN`: all position with CE values computed with PE library lower than this are considered compressions
* `--CEstats-PE-max CE_PE_MAX`: all position with CE values computed with PE library higher than this are considered expansions
* `--CEstats-MP-min CE_MP_MIN`: all position with CE values computed with MP library lower than this are considered compressions
* `--CEstats-MP-max CE_MP_MAX`: all position with CE values computed with MP library higher than this are considered expansions






LICENCE
==============
All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).
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