comparison hd.xml @ 26:15d5da04ef70 draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty

25:9e384b0741f1

The output is one PDF file with the plots of the Hamming distance, a tabular file with the data of the plot for each dataset and a tabular file with the chimeric tags. The PDF file contains several panles:

 1. This first page contains a graph representing the Hamming distance stratified by their family sizes.
 2. The second page contains the same informations as the first page but it is plotted the other way around: a family size distribution which is stratified by the Hamming distance.
 3. The third page contains the **first step** of the **chimera analysis**: HDs of the individual parts of the tags and their sums. First the tags are splitted into two halves (notated as a and b in the graph) and the minimum HD for part a (=HD a) is calculated. In the next step the data is subsetted by selecting only those tags that showed the minimum HD in half a. The HD of the second half is then calculated by comparing the b halves of the sample to the subset of halves from one step before and look for the maximum HD (=HD b'). Finally, the same approach is repeated but starts this time with the calculation of the minimum HD of part b (=HD b) followed by the calculation of the maximum HD of part a (=HD a') to identify all possible chimeras in the dataset. 
 4. The fourth page contains the **second step** of the **chimera analysis**: the absolute difference between the partial HDs (=delta HD). The HD of a chimeric reads is normally very different between its halves and therefore, the difference (=absolute delta) between those HDs should be very large, which would make it possible to identify chimeras from true molecules.
 5. The fifth page contains the **third step** of the **chimera analysis**: the relative differences of the partial HDs (=relative delta HD). Since it is not known whether the absolute difference originates due to a low and a very large HD in both halves or one half is completely identical (HD=0) to a second molecule, the relative difference is calculated by dividing the absolute difference by the HD of the whole tag (=sum of the partial HDs). The plot can be interpreted as the following: 

    - Low relative differences indicate that the total HD is almost equal split up into partial HDs. This case would be expected, if all tags originate from different molecules.
    - Higher relative differences occur either due to low total HDs and/or larger absolute differences, both things that indicate that 2 tags were originally the same tag.
    - A relative difference of 1 means that one part of the tags is identical. Since it is very unlikely that by chance two different tags have a HD of 0 between one of their parts, the HDs in the other part are probably artificially introduced (chimeric reads).

 6. The last page contains a graph representing the **HD of the chimeric tags** which is at the same time the HD of the non-identical halves of the tags with a relative difference of 1 from the previous page.

 .. class:: infomark

**Note:** 
Since the percentage of tags with a relative delta of 1 does not always represent the actual number of chimeras in the data, we have defined the number of unique chimeric tags on the last two pages below the sample size. Reasons why the counts do not have to match are the following

 1. It is possible that both halves of a chimera show a HD of 0 from two different tags. This means that their halves are identical to two different tags in the data and therefore, they have different HDs in the other part of the tags. Because it is the same tag with two different HDs we included both of them in the graphs. But when calculating the actual number of chimeras, we count the tag just once to get a more correct estimation. For better understanding see the following example where the identical part of the tag is marked with an asterix. 

    e.g. AAAAAAAAAAAT ATTCACCCTTGT	

    ***AAAAAAAAAAAT*** ATCATAGACTCT and AAAAAAAAAAAA ***ATTCACCCTTGT***

 2. When only tags of DCSs are used in the HD analysis, both family sizes of the forward and reverse strands are included in all graphs.

 
   
**About Author**
    

26:15d5da04ef70

The output is one PDF file with the plots of the Hamming distance, a tabular file with the data of the plot for each dataset and a tabular file with the chimeric tags. The PDF file contains several panles:

 1. This first page contains a graph representing the Hamming distance stratified by their family sizes.
 2. The second page contains the same informations as the first page but it is plotted the other way around: a family size distribution which is stratified by the Hamming distance.
 3. The third page contains the **first step** of the **chimera analysis**: HDs of the individual parts of the tags and their sums. First the tags are splitted into two halves (notated as a and b in the graph) and the minimum HD for part a (=HD a) is calculated. In the next step the data is subsetted by selecting only those tags that showed the minimum HD in half a. The HD of the second half is then calculated by comparing the b halves of the sample to the subset of halves from one step before and look for the maximum HD (=HD b'). Finally, the same approach is repeated but starts this time with the calculation of the minimum HD of part b (=HD b) followed by the calculation of the maximum HD of part a (=HD a') to identify all possible chimeras in the dataset. 
 4. The fourth page contains the **second step** of the **chimera analysis**: the absolute difference between the partial HDs (=delta HD). The HD of a chimeric reads is normally very different between its halves and therefore, the difference (=absolute delta) between those HDs should be very large, which would make it possible to identify chimeras from true molecules. To get a more accurate number of chimeric tags in the later steps, the maximum difference will be selected since the calculation of the HDs of the parts was performed twice for each tag in the third step.
 5. The fifth page contains the **third step** of the **chimera analysis**: the relative differences of the partial HDs (=relative delta HD). Since it is not known whether the absolute difference originates due to a low and a very large HD in both halves or one half is completely identical (HD=0) to a second molecule, the relative difference is calculated by dividing the absolute difference by the HD of the whole tag (=sum of the partial HDs). The plot can be interpreted as the following: 

    - Low relative differences indicate that the total HD is almost equal split up into partial HDs. This case would be expected, if all tags originate from different molecules.
    - Higher relative differences occur either due to low total HDs and/or larger absolute differences, both things that indicate that 2 tags were originally the same tag.
    - A relative difference of 1 means that one part of the tags is identical. Since it is very unlikely that by chance two different tags have a HD of 0 between one of their parts, the HDs in the other part are probably artificially introduced (chimeric reads).

 6. The last page contains a graph representing the **HD of the chimeric tags** which is at the same time the HD of the non-identical halves of the tags with a relative difference of 1 from the previous page.

 .. class:: infomark

**Note:** 
It is possible that both halves of a chimera show a HD of 0 from two different tags. This means that their halves are identical to two different tags in one part of the tag and therefore, they show different HDs in the second part of the tag. In such a case the maximum HD will be selected in the plots but they are notated as the following example in the output file containing the chimeric tags (the identical part of the tag is marked with an asterix):

    e.g. AAAAAAAAAAAT ATTCACCCTTGT	

    ***AAAAAAAAAAAT*** ATCATAGACTCT and AAAAAAAAAAAA ***ATTCACCCTTGT***

 
   
**About Author**