Changes between Version 12 and Version 13 of SOPs/atac_Seq

Timestamp:

08/14/20 11:12:33 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -71 +71 @@
 {{{
 
-# need to sort by name
-samtools sort -n -T abc bowtie/ATAC.bam >ATAC_sortedByName.bam"
-Genrich -e chrM -j -r -v -t ATAC_sortedByName.bam  -o peaks/ATAC_peak  -f peaks/ATAC_log
+# Start by sorting mapped reads by read name
+samtools sort -n bowtie/ATAC.bam > ATAC_sortedByName.bam
+# Run Genrich
+Genrich -e chrM -j -r -v -t ATAC_sortedByName.bam -o peaks/ATAC_peak -f peaks/ATAC_log
 
-Where
--j      ATAC-seq mode (must be specified)  intervals are interpreted that are centered on transposase cut sites (the ends of each DNA fragment). Only properly paired alignments are analyzed by default
--r      Remove PCR duplicates
+where
+-j              ATAC-seq mode (must be specified)  intervals are interpreted that are centered on transposase cut sites (the ends of each DNA fragment). Only properly paired alignment are analyzed by default
+-r              Remove PCR duplicates
 -d <int>        Expand cut sites to the given length (default 100bp)
--e <arg>        Chromosomes (reference sequences) to exclude. Can be a comma-separated list, e.g. -e chrM,chrY.
+-e <arg>        Chromosomes (reference sequences) to exclude. Can be a comma-separated  list, e.g. -e chrM,chrY.
 -E <file>       Input BED file(s) of genomic regions to exclude, such as 'N' homopolymers or high mappability regions
--t  <file>       Input SAM/BAM file(s) for experimental sample(s)
--o  <file>       Output peak file (in ENCODE narrowPeak format)
--f <LOG>        Those who wish to explore the results of varying the peak-calling parameters (-q/-p, -a, -l, -g) should consider having Genrich produce a log file when it parses the SAM/BAM files (for example, with -f <LOG> added to the above command). Then, Genrich can call peaks directly from the log file with the -P option:
-                        Genrich  -P  -f <LOG>  -o <OUT2>  -p 0.01  -a 200  -v
+-t <file>       Input SAM/BAM file(s) for experimental sample(s)
+-o <file>       Output peak file (in ENCODE narrowPeak format)
+-f <LOG>        Those who wish to explore the results of varying the peak-calling parameters (-q/-p, -a, -l, -g) should consider having Genrich produce a log file when it parses the SAM/BAM files (for example, with -f <LOG> added to the above command). Then, Genrich can call peaks directly from the log file with the -P option: Genrich -P -f <LOG> -o <OUT2> -p 0.01  -a 200 -v
 }}}