comparison hd.xml @ 24:3bc67ac46740 draft

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

23:ffd105ac12fb

 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).

24:3bc67ac46740

 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).