Changes between Version 104 and Version 105 of SOPs/atac_Seq

Timestamp:

10/31/23 09:33:57 (17 months ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -53 +53 @@
 # Use alignmentSieve from [[https://deeptools.readthedocs.io/en/develop/|DeepTools]]
 #   "--samFlagInclude 2" => keep only properly paired reads
-alignmentSieve -b file.bam --minMappingQuality 30 --samFlagInclude 2 -o MAPQ30.bam
+alignmentSieve -b Mapped_reads.bam --minMappingQuality 30 --samFlagInclude 2 -o Mapped_reads.MAPQ30.bam
 
 # Use samtools (for single-end reads)
-samtools view -b -q 30 file.bam > MAPQ30.bam
+samtools view -b -q 30 Mapped_reads.bam > Mapped_reads.MAPQ30.bam
 }}}
 
   * Remove duplicates with Picard's 'MarkDuplicates' or 'samtools rmdup'.
 {{{
-java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=foo.bam O=noDups.bam M=foo.marked_dup_metrics.txt REMOVE_DUPLICATES=true
+java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=Mapped_reads.bam O=Mapped_reads.noDups.bam M=foo.marked_dup_metrics.txt REMOVE_DUPLICATES=true
 }}}
   * Check deduplication level with [[http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads | 'fastqc']].
@@ -67 +67 @@
   * Remove reads mapped to mitochondria.
 {{{
-samtools view -h file.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > file.sorted.bam
+samtools view -h Mapped_reads.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > Mapped_reads.sorted.bam
 }}}
 
   * Index the bam file.
 {{{
-samtools index file.sorted.bam
+samtools index Mapped_reads.sorted.bam
 }}}
 
@@ -141 +141 @@
 . /nfs/BaRC_Public/conda/start_barc_conda
 }}}
-      * Before running ENCODE pipeline, verify there is no preexisting      conda startup code with the command below:
+      * Before running the ENCODE pipeline, verify there is no preexisting      conda startup code with the command below:
 {{{
 conda env list
 }}}
        You have no preexisting conda if you get "conda: command not found". Otherwise, log out, log back in, start the new conda instance, and activate encode-atac-seq-pipeline
-      * Ignore the developer's instructions, use your home directory for conda and the pipeline.
+      * Ignore the developer's instructions and use your home directory for conda and the pipeline.
 {{{
 conda activate encode-atac-seq-pipeline
 }}}
-      * Run. Files could be url or fullpath. [[https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md | Detail information about .json file]]
+      * Run. Files could be url or fullpath. [[https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md | Detailed information about .json file]]
 {{{
 caper run /nfs/BaRC_Public/atac-seq-pipeline/atac.wdl -i sample.json