Filter duplicates with picard

Question

[María José]

Hi, I have tried to use Picard and filter duplicates in Illumina data after alignment, but it encounters memory issues. I've tried to increase memory with --mem 50 when submitting the job to the queue manager. Would it be advisable to decrease the max_records_in_ram? if so, would this change affect the subsequent results? Any guidance on this topic would be greatly appreciated.

java -jar picard.jar MarkDuplicates I="./U2OS_sorted.bam" O="./U2OS_sorted_duplicates.bam" M="./U2OS_sorted_metrics_dup.txt" ASSUME_SORT_ORDER=coordinate

[Pierre Lindenbaum]

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Analyze read lengths in Illumina data Process Illumina Sequencing Data. Determine type of Pacbio read Extract aligned positions from reads how to see Pacbio reads in IGV

Answer 1

[Pierre Lindenbaum]

increase the java memory

java -Xmx10G -jar picard.jar MarkDuplicates ....

[María José]

Hi Pierre Lindenbaum, thank for your assistance. Now, Picard functions without memmory issues.However, I encounter a new error when I tried to run MarkDuplicates. I've used validateSamFile and some reads have problems:

ERROR: MISSING_READ_GROUP: 1
WARNING: RECORD_MISSING_READ_GROUP: 95,545,542

I think this issue could be resolved with AddOrReplaceReadGroups but I don't know what to indicate in the parameters: RGID=id(1 number ?), RGSM=name(HCT117 (cell line?), RGPU=unit, and RGPL=ILLUMINA. The ID of the reads is as follows: LH00587:112:22LM2WLT4:1:1101:4868:1028.

[Pierre Lindenbaum]

that is another question.

[Pierre Lindenbaum]

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