Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • example for using Picard removing duplicate reads?

    Does anybody can give me such example?

    java -jar ~/bin/picard/MarkDuplicates.jar REMOVE_DUPLICATES=true METRICS_FILE=dup.txt INPUT=accepted_hits.bam OUTPUT=remove_accepted_hits.bam

    Thank you very much.

  • #2
    Hi,
    I usually increase the RAM used, change the validation stringency and define a tmp dir.

    My example will look like this:
    java -Xmx4g -jar ~/bin/picard/MarkDuplicates.jar INPUT=accepted_hits.bam OUTPUT=remove_accepted_hits.bam METRICS_FILE=dup.txt VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true TMP_DIR=/tmp

    Comment


    • #3
      Thank you for your suggestions.
      I am doing RNA-seq data analysis. I am still not very sure it is neccessary to remove the duplication or not.

      Comment


      • #4
        When I used picard to remove dulications, I used fastqc to check. It still have a high duplication level (63%). Why?

        Comment


        • #5
          Maybe your library has low complexity?

          Comment


          • #6
            I'm having trouble with this MarkDuplicates. I hope someone could help. When I didn't include the "VALIDATION_STRINGENCY=LENIENT" I got an error saying "Mate Alignment start should be !=0 because reference name != *". But when I included it there's these error line that keeps changing extremely but its running. Is this normal?
            HTML Code:
            <a href="http://www.mylivesignature.com" target="_blank"><img src="http://signatures.mylivesignature.com/54489/368/747C8ACDDDB7178899D9E6BAA765C3FC.png" style="border: 0 !important; background: transparent;"/></a>

            Comment


            • #7
              Originally posted by fabrice View Post
              Thank you for your suggestions.
              I am doing RNA-seq data analysis. I am still not very sure it is neccessary to remove the duplication or not.
              I think in RNAseq is normal to see reads piling up at the same position (i.e. duplicates), especially in highly expressed genes and/or with high sequencing depth. So I don't think it is recommendable to remove duplicates. But see also this thread for longer discussion http://seqanswers.com/forums/showthread.php?t=6854.

              Comment


              • #8
                I need some suggestion about the mark duplicates command using picard tool, can anyone tell me if in the input and out label we can specify path as well or not? as I want to run 6 samples together so I will use it as a script and execute all of them one by one so can I specify path in the input and out like below.

                java -Xmx14g -jar /data/PGP/gmelloni/picard-tools-1.84/picard-tools-1.84/MarkDuplicates.jar INPUT=/test/exome/input/SRR062634.sorted.bam OUTPUT=/test/exome/results/SRR062634_marked.sorted.bam REMOVE_DUPLICATES=False METRICS_FILE=metricN.log ASSUME_SORTED=True VALIDATION_STRINGENCY=LENIENT

                Comment


                • #9
                  Originally posted by vd4mindia View Post
                  can anyone tell me if in the input and out label we can specify path as well or not?

                  java -Xmx14g -jar /data/PGP/gmelloni/picard-tools-1.84/picard-tools-1.84/MarkDuplicates.jar INPUT=/test/exome/input/SRR062634.sorted.bam OUTPUT=/test/exome/results/SRR062634_marked.sorted.bam REMOVE_DUPLICATES=False METRICS_FILE=metricN.log ASSUME_SORTED=True VALIDATION_STRINGENCY=LENIENT
                  I'm pretty sure you can specify the path, just try and see...

                  Comment


                  • #10
                    Yes I have queued a script and its still running. Since am working from home my intenet is a bit weak so have to run script in cluster and cant asses the command line script so I was asking but it seems to work for me. Will keep posted if its successful or failed.

                    Comment

                    Latest Articles

                    Collapse

                    • seqadmin
                      Exploring the Dynamics of the Tumor Microenvironment
                      by seqadmin




                      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                      07-08-2024, 03:19 PM
                    • seqadmin
                      Exploring Human Diversity Through Large-Scale Omics
                      by seqadmin


                      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                      06-25-2024, 06:43 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, Today, 07:20 AM
                    0 responses
                    13 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-16-2024, 05:49 AM
                    0 responses
                    33 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-15-2024, 06:53 AM
                    0 responses
                    37 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-10-2024, 07:30 AM
                    0 responses
                    41 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X