| 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 |
