RELEASE NOTES FOR HICUP V0.3.0 (02 November 2012) ------------------------------------------------- HiCUP v0.3.0 is a major update incorporating the changes described below. - hicup_sorter removed from the pipeline. Users should now de-multiplex samples using other software. - The pipeline determines automatically the FASTQ format (e.g. Sanger) adopted if this was not specified by the user. It may not always be possible to determine this unambiguously and in such circumstances the pipeline selects the most likely option. - The pipeline will try to determine the path to Bowtie if this is not specified by the user. Also, fixed a bug in how HiCUP identifies the location of SAMtools. - Improved how the pipeline checks Bowtie indices have been specified correctly by the user. RELEASE NOTES FOR HICUP V0.2.2 (03 August 2012) ----------------------------------------------- HiCUP v0.2.2 is a minor update adding the functionality described below. - The mapping process is now less memory intensive, with Bowtie --chunkmbs lowered from 1024 to 512. Also, reads shorter than 20bps are no longer passed to Bowtie. - Fixed bug preventing HiCUP processing files in a separate folder from the hicup.conf configuration file. - The hicup master script terminates immediately if another pipeline script dies. RELEASE NOTES FOR HICUP V0.2.1 (19 July 2012) --------------------------------------------- HiCUP v0.2.1 is a minor update adding the functionality described below. - The hicup_filter script now calculates the number of di-tags whose alignment to the reference genome suggests they were created by a single restriction fragment circularizing and ligating to itself, and then following sonication forms a liner molecule containing the modified Hi-C restriction site. These di-tags were previously classified as 'Same Fragment' di-tags, but this category now comprises all di-tags in which both reads map to the same restriction fragment except those classified as derived from circularized molecules. - The hicup_filter summary file now reports the number of di-tags falling within each category, not the percentage summary. RELEASE NOTES FOR HICUP V0.2.0 (26 June 2012) --------------------------------------------- HiCUP v0.2.0 is a major update providing extra functionality in addition to the removal of several bugs. The most significant changes are described below. - Addition of a new script ('hicup_deduplicator') at the end of the pipeline for removing duplicate di-tags (most probably PCR artefacts). The script generates a text file summarising the results, along with a pie chart (*.png format) of the cis/trans ratio of di-tags present in the final dataset. - hicup_mapper and hicup_pairer combined into a single script called 'hicup_mapper'. In addition to reporting Bowtie mapping efficiencies, the script also reports the percentage read pairs in which both forward and reverse reads could be aligned to the reference genome. - hicup_filter, when processing Hi-C data generated using the Hi-C sonication protocol, now rejects di-tags on the basis of size AFTER all other filters have been passed. - hicup_filter produces a less verbose summary file and produces pie charts of the results (*.png format). - hicup_filter modified so when following the sonication protocol it identifies and rejects di-tags containing re-ligated fragments, not simply those on adjacent fragments. It does this by checking that the fragments are adjacent (as before) and in the same orientation - which means the forward and reverse reads will be on opposite strands (+ and -). - hicup_truncater now reports the average length of a truncated sequence. - Fixed a bug causing hicup_digester to only process the last chromosome in a file containing multiple chromosomes. RELEASE NOTES FOR HICUP V0.1.1 ------------------------------ HiCUP v0.1.1 is an alpha release and as such is still a work in progress. Although the core functionality of the program should all now be present it is very much still a work in progress and you should bear this in mind when using the software. Things may break and there may be bugs which will need to be resolved Having said that, we are using the software for real work so it should be useful in its current state. The functionality of HiCUP is not yet complete. As such we are keen to hear from other groups if they have ideas for useful functions which could be added. We have initially developed the functions to support the types of analysis we require, but there are probably many other applications which could be supported by the core HiCUP framework.