Changes between Initial Version and Version 1 of SOPs/HiChIP

Timestamp:

01/07/21 16:25:08 (4 years ago)

Author:

twhitfie

Comment:

--

SOPs/HiChIP

@@ +1 @@
+== Using Hi-C to capture chromatin structure ==
+
+
+The  [[https://science.sciencemag.org/content/326/5950/289 | Hi-C method]] Hi-C method generalizes earlier experimental techniques, such as 3C or 5C,  for characterizing contacts between specific chromosomal loci, to enable unbiased identification of chromatin interactions across an entire genome.  Two software pipelines for analyzing data from Hi-C experiments are [[https://github.com/aidenlab/juicer | juicer]] and  [[https://github.com/nservant/HiC-Pro | HiC-Pro]]. An example for using HiC-Pro on Whitehead computing resources with data collected with a kit from Arima Genomics is outlined below. Note that in this example, a reference genome is used that excludes unlocalized or unplaced contigs from the assembly.  This choice is taken to ease downstream analysis.  Please see the HiC-Pro [[http://nservant.github.io/HiC-Pro/ | documentation]] for additional examples.
+
+=== Analysis outline ===
+ * [#SetConfig Set up the HiC-Pro configuration file]
+ * [#Submit Submit data processing to the LSF batch queue]
+ * [#ContactMaps Generate contact map visualizations from processed Hi-C data]
+
+=== [=#SetConfig Set up the configuration file] ===
+
+  * The configuration file (here called config.txt) dictates essential settings for the analysis.  In this example, human samples have been sequenced and an e-mail will be sent to "user at wi.mit.edu" on job completion.
+
+{{{
+# Please change the variable settings below if necessary
+
+#########################################################################
+## Paths and Settings  - Do not edit !
+#########################################################################
+
+TMP_DIR = tmp
+LOGS_DIR = logs
+BOWTIE2_OUTPUT_DIR = bowtie_results
+MAPC_OUTPUT = hic_results
+RAW_DIR = rawdata
+
+#######################################################################
+## SYSTEM - PBS - Start Editing Here !!
+#######################################################################
+N_CPU = 8
+LOGFILE = hicpro.log
+
+JOB_NAME = HiC
+JOB_MEM = 20gb
+JOB_WALLTIME = 12:00:00
+JOB_QUEUE = batch
+JOB_MAIL = user@wi.mit.edu
+
+#########################################################################
+## Data
+#########################################################################
+
+PAIR1_EXT = _R1
+PAIR2_EXT = _R2
+
+#######################################################################
+## Alignment options
+#######################################################################
+
+FORMAT = phred33
+MIN_MAPQ = 0
+
+BOWTIE2_IDX_PATH = /nfs/genomes/human_hg38_dec13_no_random/bowtie
+BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
+BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder
+
+#######################################################################
+## Annotation files
+#######################################################################
+
+REFERENCE_GENOME = hg38
+GENOME_SIZE = /nfs/genomes/human_hg38_dec13_no_random/anno/chromInfo.txt
+
+#######################################################################
+## Allele specific
+#######################################################################
+
+ALLELE_SPECIFIC_SNP = 
+
+#######################################################################
+## Digestion Hi-C
+#######################################################################
+
+GENOME_FRAGMENT = /nfs/genomes/human_hg38_dec13/arima/hg38_GATC_GANTC.bed
+LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC
+MIN_FRAG_SIZE = 10
+MAX_FRAG_SIZE = 100000
+MIN_INSERT_SIZE = 100
+MAX_INSERT_SIZE = 1000
+
+#######################################################################
+## Hi-C processing
+#######################################################################
+
+MIN_CIS_DIST =
+GET_ALL_INTERACTION_CLASSES = 1
+GET_PROCESS_SAM = 1
+RM_SINGLETON = 1
+RM_MULTI = 1
+RM_DUP = 1
+
+#######################################################################
+## Contact Maps
+#######################################################################
+
+BIN_SIZE = 1000 5000  10000 20000 50000 100000
+MATRIX_FORMAT = upper
+
+#######################################################################
+## ICE Normalization
+#######################################################################
+MAX_ITER = 100
+FILTER_LOW_COUNT_PERC = 0.02
+FILTER_HIGH_COUNT_PERC = 0
+EPS = 0.1
+}}}
+
+
+
+=== [=#Submit Submit data processing to the LSF batch queue] ===
+
+The essential command to include when submitting HiC-Pro computations to the LSF batch queue is given below, where config.txt is located in the working directory, as are the rawdata and hicproOut subdirectories.  As also specified in the (config.txt) configuration file, HiC-Pro will create bowtie_results and hic_results subdirectories beneath hicproOut.
+{{{
+/usr/local/HiC-Pro_2.11.1/bin/HiC-Pro -c config.txt -i rawdata/ -o hicproOut
+}}}
+
+=== [=#ContactMaps Generate contact map visualizations from processed Hi-C data] ===
+
+Hi-C experiments enable the visualization of chromatin contact maps.  Output from HiC-Pro can be translated into contact maps using [[http://bioconductor.org/packages/release/bioc/html/HiTC.html | HiTC]], the [[https://www.aidenlab.org/juicebox/ | juicebox viewer]] or [[https://github.com/kcakdemir/HiCPlotter | HiCPlotter ]].  To use the juicebox viewer, the HiC-Pro output must first be processed using /usr/local/HiC-Pro_2.11.1/bin/utils/hicpro2juicebox.sh.  The example below illustrates how to use HiCPlotter to visualize the contact map for the Y chromosome using a 100 kb resolution and naming the graphical output file with a "cellType" prefix.
+{{{
+python2 /usr/local/bin/python2.7/HiCPlotter.py -f /path/to/hic_results/matrix/sample1/iced/100000/sample1_100000_iced.matrix -chr chrY -o cellType -n " " -r 100000 -tri 1 -bed /path/to/hic_results/matrix/sample1/raw/100000/sample1_100000_abs.bed -mm 6
+}}}