RELEASE NOTES FOR HICUP v0.7.4 (18 June 2020) --------------------------------------------- HiCUP v0.7.4 is a minor update incorporating the changes described below: -Fixed bug when specifying a cut-site containing an N (any nucleotide). The script hicup_truncater used to incorporate such Ns into the FASTQ truncated read. This is now fixed and no longer occurs. -HiCUP now uses CIGAR string information when positioning reads to restriction fragments and during the de-duplication process. -Added scripts for GitHub Actions unit testing. -Added a HiCUP Singularity recipe to the Misc folder. RELEASE NOTES FOR HICUP v0.7.3 (13 May 2020) -------------------------------------------- HiCUP v0.7.3 is a minor update incorporating the changes described below: -Added hicup2juicer to make HiCUP output compatible with Juicer. -Modification to hicup_deduplicator output so files strictly adhere to SAM/BAM format. -Fixed bug preventing --nofill option from working. -No longer reports Bowtie2 message concerning gzbuffer changes. RELEASE NOTES FOR HICUP v0.7.2 (15 January 2019) ------------------------------------------------ HiCUP v0.7.2 is a minor update incorporating the changes described below: -Fixed bug causing output files to not strictly adhere to SAM/BAM format. RELEASE NOTES FOR HICUP v0.7.1 (12 November 2018) ------------------------------------------------- HiCUP v0.7.1 is a minor update incorporating the changes described below: -Added the option --arima to HiCUP Digester, to generate digest files compatible with the Arima protocol. RELEASE NOTES FOR HICUP v0.7.0 (26 October 2018) ------------------------------------------------ HiCUP v0.7.0 is a major update incorporating the changes described below: HiCUP can now process restriction enzymes that cut at different sites. Such sequences contain an "N" within the restriction enzyme recognition site to denote the four bases (AGCT). Thanks to Rola Dali, Edouard Henrion and Mathieu Bourgey (McGill University) for adding this feature. RELEASE NOTES FOR HICUP v0.6.1 (10 May 2018) ---------------------------------------------- HiCUP v0.6.1 is a minor update incorporating the changes described below: -Bowtie2 may now align reads using more than one thread (while preserving the input/output read order), thereby reducing processing times. The number of threads allocated to Bowtie2 will be the number of threads specified by the user divided by the number of files processed. -Fixed bug causing HiCUP Mapper to try to read beyond the end of a mapped reads SAM file, consequently causing the script to crash. RELEASE NOTES FOR HICUP v0.6.0 (23 April 2018) ---------------------------------------------- HiCUP v0.6.0 is a major update incorporating the changes described below: -Parameters adjusted for HiCUP mapper in determining what constitutes a multi-mapping read, when using Bowtie2 as the aligner. RELEASE NOTES FOR HICUP v0.5.10 (26 October 2017) ------------------------------------------------- HiCUP v0.5.10 is a minor update incorporating the changes described below: -Fixed bug causing hicup_mapper to not pair a small proportion of valid reads. RELEASE NOTES FOR HICUP v0.5.9 (15 September 2016) -------------------------------------------------- HiCUP v0.5.9 is a minor update incorporating the changes described below: -Modified HiCUP Deduplicator so it may process genomes comprising hundreds of chromosomes (e.g. genome assemblies) -Added script Misc/get_captured_reads for identifying on/off target di-tags in capture Hi-C datasets -Fixed bug when running hicup_truncater independently, causing the script to interpret NoFill:0 in the config file as effectively NoFill:1 RELEASE NOTES FOR HICUP v0.5.8 (19 October 2015) ------------------------------------------------ HiCUP v0.5.8 is a minor update incorporating the changes described below: - Fixed bug preventing an odd number of files being specified when using a configuration file with hicup_digester, hicup_filter or hicup_deduplicator. RELEASE NOTES FOR HICUP v0.5.7 (18 June 2015) --------------------------------------------- HiCUP v0.5.7 is a minor update incorporating the changes described below: - Fixed bug preventing whole pipeline running to completion if --outdir is set to a folder other than the current working directory. RELEASE NOTES FOR HICUP v0.5.6 (09 June 2015) --------------------------------------------- HiCUP v0.5.6 is a minor update incorporating the changes described below: - Fixed bug preventing, when multiple samples are processed, the generation of HTML summary reports and the text file auditing the progress of read pairs through the entire pipeline. RELEASE NOTES FOR HICUP v0.5.5 (20 May 2015) -------------------------------------------- HiCUP v0.5.5 is a minor update incorporating the changes described below: - HiCUP produces a text file auditing the progress of read pairs through the entire pipeline for all samples processed. - Added the 'Conversion' folder, containing scripts for converting HiCUP BAM/SAM output into formats compatible with GOTHiC, Homer, Hicpipe and Fit-Hi-C. Fixed bug preventing users specifying two --re1 restriction enzymes (i.e. the enzymes that create the Hi-C ligation junctions). RELEASE NOTES FOR HICUP v0.5.4 (01 April 2015) ---------------------------------------------- HiCUP v0.5.4 is a minor update incorporating the changes described below: - HiCUP Digester checks the first line of each input file begins with a valid FASTA header. - Fixed bug causing HiCUP to ignore choice of aligner. - HiCUP output compatible with SamTools release (v1.2), which is more strict with regard to the PG headers in a BAM/SAM file. - Fixed bug causing files to be compressed if zip:0 selected in a configuration file. - Fixed bug causing --re2 option sequence (i.e. not --re1 sequence) to be used to truncate reads prior to mapping. - Should one or more sample contain no valid di-tags the pipeline would produce no HTML summary files, even for samples containing valid di-tags. This no longer happens, instead the script displays a warning message reporting samples not progressing through the pipeline and produces HTML for samples containing valid di-tags. - Improved documentation by creating Markdown files. These were added to the 'Documentation' folder. The HiCUP Manual and QuickStart PDF files were deleted. RELEASE NOTES FOR HICUP v0.5.3 (31 December 2014) ------------------------------------------------- HiCUP v0.5.3 is a minor update incorporating the changes described below: - HiCUP attempts to intelligently name files as the pipeline proceeds. Please Note: To avoid passing HiCUP input files with identical names prior to the filename extension. For example, the files 'sample.fa' and 'sample.fastq' would produce files with identical names as the pipeline progresses. This problem could be overcome by renaming one the files to 'sample2.fa'. To minimise inconvenience, HiCUP will immediately produce a warning message and not run if the input filenames are too similar. RELEASE NOTES FOR HICUP v0.5.2 (22 November 2014) ------------------------------------------------- HiCUP v0.5.2 is a minor update incorporating the changes described below: - When running the whole pipeline, a folder may be specified to which all intermediate files are written. These files are deleted after the hicup_deduplicator script has terminated. - FASTQ format now specified differently, valid options are: Sanger, Solexa_Illumina_1.0, Illumina_1.3 or Illumina_1.5 - All configuration files kept in the 'config_files' folder. - hicup_digester may be passed lowercase characters denoting the restriction enzyme recognition site. - Pipeline no longer terminates if SAM Tools in not installed. RELEASE NOTES FOR HICUP v0.5.1 (02 November 2014) ------------------------------------------------- HiCUP v0.5.1 is a minor update incorporating the changes described below: - hicup_deduplicator now accepts --threads as an argument. RELEASE NOTES FOR HICUP v0.5.0 (01 October 2014) ------------------------------------------------- HiCUP v0.5.0 is a major update incorporating the changes described below: - HiCUP compatible with Bowtie2. - To reduce mis-mapping, HiCUP no longer uses --strata as a parameter when aligning with Bowtie. - Perl module GD::Graph is no longer a dependency since the pipeline now uses R to generate figures. - The scripts ‘hicup’, ‘hicup_trunacter’ and ‘hicup_mapper’ all require file pairs as input. Such pairs should now be placed on adjacent lines in their respective configuration files. (Previous versions of HiCUP required paired files to be placed on the same line, separated using the pipe (‘|’) character. HiCUP still accepts filename pairs in this deprecated format.) - Command line arguments can be used in conjunction with a configuration file. Parameters set using the command line will override those set using a configuration file. - Fixed bug causing HiCUP only being able to process files in the current working directory. RELEASE NOTES FOR HICUP v0.4.2 (27 November 2013) ------------------------------------------------- HiCUP v0.4.2 is a minor update incorporating the changes described below: - Pipeline produces di-tag length (prior to filtering) distribution plots in the HTML document and as a separate GD::Graph line plot. - Pipeline produces an HTML report when following the double-digest protocol. - HTML file reports percentage unique di-tags following de-duplication. - HiCUP version number and pipeline parameters are printed in the headers of the SAM/BAM files. - User can specify hi-c ligation sequences directly via hicup.conf - Fixed bug causing HTML reports not to be written if a single sample did not pass completely through the pipeline. - Fixed bug preventing 'longest:' or 'shortest:' config option being left blank in hicup.conf RELEASE NOTES FOR HICUP v0.4.1 (23 September 2013) -------------------------------------------------- HiCUP v0.4.1 is a minor update incorporating the changes described below: - Fixed bug causing results from different datasets to become mixed in the HTML report. - Improved HTML report layout. RELEASE NOTES FOR HICUP v0.4.0 (10 September 2013) -------------------------------------------------- HiCUP v0.4.0 is a major update incorporating the changes described below: - A di-tag is defined by each of its constituent reads and each read is now defined by 1) the position in the reference genome to which the first base of the sequence read (putative sonication cut site) map; and 2) the orientation of the sequence read with respect to the reference genome. The read end position is no longer considered. - Fixed bug in hicup_deduplicator preventing it identifying all duplicates if the sequencing run was performed with a different number of cycles. - Added --nofill option to hicup_truncater (and consequently hicup) allowing users to specify that a fill-in of sticky ends was not performed. - Made slight adjustment to hicup_truncator to prevent division by zero errors when working out the %truncation rate. - hicup_truncater now truncates upstream of the restriction enzyme recognition site, not at the restriction enzyme cut site. - hicup_mapper now reports the number of reads that were too short to be sent to Bowtie. The mapping efficiency will refer to: (100 * unique alignments) / (reads too short to send to Bowtie + reads sent to Bowtie). - hicup_filter now discriminates between same-fragment dangling ends and same-fragment internal. - HiCUP master script edited so the file processes all the reads in a file to determine FASTQ quality scores. - Added a check in the pipeline to confirm the number of forward and reverse reads are the same in the FASTQ file pairs (some users appear to filter reads in some way prior passing to HiCUP). - Users can now specify an output directory to which output files are written. - All summary files now display the same datestamp. - HiCUP sonication protocol now generates an HTML report summarising the results of each file processed. 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 option --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 mind when running the software.