Changes between Version 13 and Version 14 of SOPs/atac_Seq

Timestamp:

08/14/20 11:14:07 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -8 +8 @@
  * [#preprocess Pre-process reads](remove adapters and other "contamination")
  * [#map Map reads to the genome] (with an unspliced mapping tool)
- * [#Run quality control and calculate QC metrics]
+ * [#QC Run quality control and calculate QC metrics] 
  * [#call_peaks Call ATAC-seq "peaks"] with a high coverage of mapped reads
  * Analyze peak regions for binding motifs
@@ -71 +71 @@
 {{{
 
-# 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
+# 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
 
-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
+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
 -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
 }}}
 
@@ -106 +106 @@
 
 
-=== [=#Run quality control and calculate QC metrics] ===
+=== [=#QC Run quality control and calculate QC metrics] ===
+
 * Fragment size distribution with ATACseqQC R package:
 {{{