| c8b8c79 | Benjamin Emert | 26 March 2020, 17:37:11 UTC | Updated reorganizeBasespaceFiles.py to better parse samples with same first index (e.g. sample 1 and sample10) | 26 March 2020, 17:37:11 UTC |
| d64c711 | Eric Sanford | 10 October 2019, 18:04:36 UTC | added location of hg19 reference files as comments to setEnvironmentVariables.sh script | 10 October 2019, 18:04:36 UTC |
| c5b88eb | Eric Sanford | 09 October 2019, 20:53:45 UTC | Updated STAR version, set default reference genome to hg38, added gene_names from gtf file when there is no HGNC symbol match, made it easier to change the reference genome by defining it in the setEnvironmentVariables.sh script. Modified some snakemake files to make that alternate pipeline almost runnable on the cluster in an interactive node. | 09 October 2019, 20:53:45 UTC |
| e650685 | pburnham50 | 30 August 2019, 13:30:07 UTC | spacing in readme file improved. | 30 August 2019, 13:30:07 UTC |
| ea45275 | pburnham50 | 30 August 2019, 12:59:30 UTC | Updated readme file. | 30 August 2019, 12:59:30 UTC |
| 0ee3936 | pburnham50 | 29 August 2019, 15:02:25 UTC | Added in pipeline to process bulk RNA-seq data. The pipeline performs trimming, QC, alignment, basic analysis, and can then compares the samples from two conditions. | 29 August 2019, 15:02:25 UTC |
| 1de88d8 | Eric Sanford | 09 August 2019, 14:51:30 UTC | Updated Ensembl to HGNC internal database readme with date of biomaRt download. Changed name of database column from hgnc.symbol to hgnc_symbol. | 09 August 2019, 14:51:30 UTC |
| cd64135 | Eric Sanford | 01 August 2019, 20:44:54 UTC | changed left join function from dplyr to plyr package to avoid duplicating ensemble gene rows when there are multiple biomaRt HGNC symbol matches | 01 August 2019, 20:44:54 UTC |
| 8328ab7 | Eric Sanford | 31 July 2019, 21:04:34 UTC | added support for paired-end reads | 31 July 2019, 21:04:34 UTC |
| f07c048 | Eric Sanford | 30 July 2019, 21:07:45 UTC | Added new folder LocalComputerScripts for scripts that should be run locally, i.e. not on the cluster. It contains an R script, normalizeMeltedCountsAndAddGeneSymbol.R, to add normalized count information and gene symbols to the final 'melted' output files from the RNA-seq pipeline | 30 July 2019, 21:07:45 UTC |
| 55f3eec | Eric Sanford | 11 January 2019, 23:18:57 UTC | Reduced number of manual steps to run pipeline, increased use of parallelization to improve speed, and compressed or deleted intermediate files to save disk space. Also updated STAR version to 2.5.2a. See updated rajlabseqtools google doc for instructions. | 11 January 2019, 23:18:57 UTC |
| 425610f | Ian Mellis | 07 January 2016, 19:25:08 UTC | Adding step to melt count data from all samples from an experiment to a single tsv file | 07 January 2016, 19:25:08 UTC |
| f8c9a19 | Ian Mellis | 07 January 2016, 18:58:37 UTC | Updates location of meltData.tsv to experiment folder rather than overall project folder | 07 January 2016, 18:58:37 UTC |
| f267e82 | Ian Mellis | 05 January 2016, 20:38:56 UTC | Updated runHTSeq.sh to call shared version of hg19.gtf, rather than Syd's in CancerSeq repo. Made a note on Rajlabseqtools pipeline doc. | 05 January 2016, 20:38:56 UTC |
| f26732e | Sydney Shaffer | 01 December 2015, 12:55:41 UTC | added post processing comparing the differential peaks in step wise analysis to the overall non-resistant versus week 4 | 01 December 2015, 12:55:41 UTC |
| e576e76 | Sydney Shaffer | 24 November 2015, 22:05:43 UTC | renamed a poorly named script | 24 November 2015, 22:05:43 UTC |
| bfa05d7 | Sydney Shaffer | 24 November 2015, 21:03:05 UTC | no message | 24 November 2015, 21:03:05 UTC |
| aa7fecf | Sydney Shaffer | 24 November 2015, 21:01:10 UTC | Added scripts for HOMER differential peak calls, gene ontology, and motif finding. | 24 November 2015, 21:01:10 UTC |
| 3ad90f0 | Sydney Shaffer | 24 November 2015, 20:55:21 UTC | Changed folder names and the appropriate files to make things a bit clearer in the ATAC analysis. Specifically, the stepThreeHOMERpeaks folder was renamed to stepFourHOMERpeaks. | 24 November 2015, 20:55:21 UTC |
| a01431b | Sydney Shaffer | 24 October 2015, 21:26:23 UTC | scripts to run HOMER peak caller | 24 October 2015, 21:26:23 UTC |
| cd8eb81 | Sydney Shaffer | 20 October 2015, 14:38:01 UTC | changed MACS2 script to run with SPMR parameter | 20 October 2015, 14:38:01 UTC |
| 8f355a9 | Sydney Shaffer | 15 October 2015, 12:18:38 UTC | made scripts to run MACS2 | 15 October 2015, 12:18:38 UTC |
| 5e9b826 | Sydney Shaffer | 13 October 2015, 15:12:07 UTC | wrote scripts to do SAM/BAM/bedGraph manipulations | 13 October 2015, 15:12:07 UTC |
| 1f85fbd | Sydney Shaffer | 13 October 2015, 12:48:21 UTC | made scripts to run bowtie2 on ATAC data | 13 October 2015, 12:48:21 UTC |
| 510a48c | Sydney Shaffer | 12 October 2015, 16:55:45 UTC | updated path to data in submission script | 12 October 2015, 16:55:45 UTC |
| 284b48d | Sydney Shaffer | 12 October 2015, 16:10:07 UTC | made setup scripts for ATAC data - these unzip fastq files and then concatenate the 4 together (from each lane) for each of the samples. | 12 October 2015, 16:10:07 UTC |
| c8f87f9 | Arjun Raj | 29 December 2014, 18:53:29 UTC | Fixed STARFLAGS so that it passes along multiple arguments. | 29 December 2014, 18:53:29 UTC |
| 30d379c | Arjun Raj | 29 December 2014, 18:24:55 UTC | Added STARFLAGS to send flags through to STAR. | 29 December 2014, 18:24:55 UTC |
| 7202e48 | Arjun Raj | 29 December 2014, 16:19:22 UTC | Added a comment in somewhere. | 29 December 2014, 16:19:22 UTC |
| b7411d3 | Sydney Shaffer | 12 November 2014, 19:52:05 UTC | added code to run the melt script at the end of step 3. | 12 November 2014, 19:52:05 UTC |
| 38ef2a6 | Sydney Shaffer | 12 November 2014, 19:50:27 UTC | Added another variable that is passed into the generate counts script | 12 November 2014, 19:50:27 UTC |
| dd2f844 | Sydney Shaffer | 12 November 2014, 19:43:18 UTC | Adding melt script for htseq output | 12 November 2014, 19:43:18 UTC |
| 2311bee | Sydney Shaffer | 11 November 2014, 19:43:50 UTC | I forgot a variable here - added it back | 11 November 2014, 19:43:50 UTC |
| 6313ee2 | Sydney Shaffer | 11 November 2014, 19:35:36 UTC | removed an redundant file | 11 November 2014, 19:35:36 UTC |
| de71c45 | Sydney Shaffer | 11 November 2014, 18:56:58 UTC | Organized the files and wrote a script that runs the samtools, bamutils, and htseq all at once. | 11 November 2014, 18:56:58 UTC |
| 5b3f6ce | Sydney Shaffer | 11 November 2014, 15:38:49 UTC | corrected path names | 11 November 2014, 15:38:49 UTC |
| fcab91d | Sydney Shaffer | 11 November 2014, 15:34:45 UTC | uploaded the correct version of runStarOnAll.sh | 11 November 2014, 15:34:45 UTC |
| 90e48cd | Sydney Shaffer | 11 November 2014, 15:28:39 UTC | changed path names to reflect moving submissionScripts to the repo folder | 11 November 2014, 15:28:39 UTC |
| 0f4bf5d | Sydney Shaffer | 11 November 2014, 15:09:26 UTC | corrected a path name | 11 November 2014, 15:09:26 UTC |
| d9be629 | Sydney Shaffer | 11 November 2014, 15:07:01 UTC | added a variable for user name - to make it easier for people to modify this script for their own work | 11 November 2014, 15:07:01 UTC |
| e8a5ca5 | Sydney Shaffer | 11 November 2014, 14:20:49 UTC | Commented out code for paired end reads | 11 November 2014, 14:20:49 UTC |
| 94c2d76 | Sydney Shaffer | 11 November 2014, 14:10:24 UTC | added a line to make the experiment folder if it does not exist | 11 November 2014, 14:10:24 UTC |
| 4e77f9a | Sydney Shaffer | 11 November 2014, 14:06:45 UTC | modified unzip script to take in any name for the different samples | 11 November 2014, 14:06:45 UTC |
| 7d5011f | Sydney Shaffer | 11 November 2014, 13:27:15 UTC | Added current scripts to submitting jobs to run star and to run star | 11 November 2014, 13:27:15 UTC |
| 8f67a7b | Arjun Raj | 19 June 2014, 12:01:10 UTC | Changed name to fastq instead of fasta | 19 June 2014, 12:01:10 UTC |
| 6311fa1 | Arjun Raj | 19 June 2014, 11:58:54 UTC | Updated unzipAndConcatenateZippedFasta to the point where it might actually work. | 19 June 2014, 11:58:54 UTC |
| d6501d6 | Arjun Raj | 18 June 2014, 17:12:56 UTC | Playing with unzip and concatenate fasta. | 18 June 2014, 17:12:56 UTC |
