update allelic counts error

docs/source/help.rst

@@ -1,11 +1,20 @@
 Troubleshooting
 ===============
 
-In case you have any issues, please open an issue on `git <https://github.com/gagneurlab/drop>`_.
+In case you have any issues, please check the previous issues on `git <https://github.com/gagneurlab/drop>`_ and the Troubleshoot section of the DROP paper. If you have a new issue, please create a new one on git.
 
-A common problem is that during the ``MAE:mae_allelicCounts`` step, if the BAM file does not have the correct ``Read Groups`` documentation both the header and reads.  
-You can often identify if the BAM file is the problem by using the command ``gatk ValidateSamFile -I path/to/bam_file.bam``
+Common errors
+-------------
 
+The ``MAE:mae_allelicCounts`` step is susceptible to fail if:
+
+1. the chromosomes styles of the reference genome and the BAM files do not match
+
+Solution: Identify the chromosomes style of the BAM file. Obtain an appropriate reference genome file and specify it in the config file.
+
+2. the BAM file does not have the correct ``Read Groups`` documentation both the header and reads. You can often identify if the BAM file has any problems by using the command ``gatk ValidateSamFile -I path/to/bam_file.bam``
+
+Solution:
 To fix this is often dependent on the individual case, but some combination of the following tools is quite helpful:  
 
 * `samtools reheader <http://www.htslib.org/doc/samtools-reheader.html>`_