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Revision Author Date Message Commit Date
c8b8c79 Updated to better parse samples with same first index (e.g. sample 1 and sample10) 26 March 2020, 17:37:11 UTC
d64c711 added location of hg19 reference files as comments to script 10 October 2019, 18:04:36 UTC
c5b88eb 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 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 spacing in readme file improved. 30 August 2019, 13:30:07 UTC
ea45275 Updated readme file. 30 August 2019, 12:59:30 UTC
0ee3936 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 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 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 added support for paired-end reads 31 July 2019, 21:04:34 UTC
f07c048 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 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 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 Updates location of meltData.tsv to experiment folder rather than overall project folder 07 January 2016, 18:58:37 UTC
f267e82 Updated 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 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 renamed a poorly named script 24 November 2015, 22:05:43 UTC
bfa05d7 no message 24 November 2015, 21:03:05 UTC
aa7fecf Added scripts for HOMER differential peak calls, gene ontology, and motif finding. 24 November 2015, 21:01:10 UTC
3ad90f0 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 scripts to run HOMER peak caller 24 October 2015, 21:26:23 UTC
cd8eb81 changed MACS2 script to run with SPMR parameter 20 October 2015, 14:38:01 UTC
8f355a9 made scripts to run MACS2 15 October 2015, 12:18:38 UTC
5e9b826 wrote scripts to do SAM/BAM/bedGraph manipulations 13 October 2015, 15:12:07 UTC
1f85fbd made scripts to run bowtie2 on ATAC data 13 October 2015, 12:48:21 UTC
510a48c updated path to data in submission script 12 October 2015, 16:55:45 UTC
284b48d 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 Fixed STARFLAGS so that it passes along multiple arguments. 29 December 2014, 18:53:29 UTC
30d379c Added STARFLAGS to send flags through to STAR. 29 December 2014, 18:24:55 UTC
7202e48 Added a comment in somewhere. 29 December 2014, 16:19:22 UTC
b7411d3 added code to run the melt script at the end of step 3. 12 November 2014, 19:52:05 UTC
38ef2a6 Added another variable that is passed into the generate counts script 12 November 2014, 19:50:27 UTC
dd2f844 Adding melt script for htseq output 12 November 2014, 19:43:18 UTC
2311bee I forgot a variable here - added it back 11 November 2014, 19:43:50 UTC
6313ee2 removed an redundant file 11 November 2014, 19:35:36 UTC
de71c45 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 corrected path names 11 November 2014, 15:38:49 UTC
fcab91d uploaded the correct version of 11 November 2014, 15:34:45 UTC
90e48cd changed path names to reflect moving submissionScripts to the repo folder 11 November 2014, 15:28:39 UTC
0f4bf5d corrected a path name 11 November 2014, 15:09:26 UTC
d9be629 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 Commented out code for paired end reads 11 November 2014, 14:20:49 UTC
94c2d76 added a line to make the experiment folder if it does not exist 11 November 2014, 14:10:24 UTC
4e77f9a modified unzip script to take in any name for the different samples 11 November 2014, 14:06:45 UTC
7d5011f Added current scripts to submitting jobs to run star and to run star 11 November 2014, 13:27:15 UTC
8f67a7b Changed name to fastq instead of fasta 19 June 2014, 12:01:10 UTC
6311fa1 Updated unzipAndConcatenateZippedFasta to the point where it might actually work. 19 June 2014, 11:58:54 UTC
d6501d6 Playing with unzip and concatenate fasta. 18 June 2014, 17:12:56 UTC
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