Using nudup on Elzar
nudup.py is a Python script that marks/removes PCR introduced duplicated molecules based on the molecular tagging technology used in Tecan products. It can be used for both single-end and paired-end reads. It requires a SAM/BAM file and a FASTQ file as inputs.
nudup.py can be obtained here
> git clone https://github.com/tecangenomics/nudup.gitIt is clear from the README that nudup.py has only been tested on legacy software versions.
For expected behavior, I recommend configuring your environment to match the stated prerequisites.
> module load EBModules> module load SAMtools/1.14-GCC-10.3.0> module load Python/2.7.16-GCCcore-8.3.0> which python/grid/it/data/elzar/easybuild/software/Python/2.7.16-GCCcore-8.3.0/bin/pythonTry running nudup.py without any options to ensure there are no errors:
> python nudup.pyusage: nudup.py [-2] [-f INDEX.fq|READ.fq] [-o OUT_PREFIX] [-s START] [-l LENGTH] [-T TEMP_DIR] [--old-samtools] [--rmdup-only] [-v] [-h] IN.sam|IN.bamnudup.py: error: too few argumentsnudup.py works with aligned and sorted BAM or SAM files from next-generation sequencing (NGS).
As a test, I cloned this repository which contained some test BAM files.
> python nudup.py -o test_bam_dedup ../rnaseq/test/hisat2_k20.bam2023-05-11 14:52:36,599 [ INFO] - Deduplicating NuGEN single end reads...2023-05-11 14:52:36,654 [ INFO] - Processing sorted SAM/BAM with molecular tag sequence in read name (assumes sorted)2023-05-11 14:52:36,929 [ INFO] - Aligned count: 242902023-05-11 14:52:36,929 [ INFO] - Unaligned count: 02023-05-11 14:52:36,929 [ INFO] - Molecular tag dups count: 0 (0.0000 rate)2023-05-11 14:52:36,929 [ INFO] - Deduplication success.2023-05-11 14:52:36,929 [ INFO] - Created output file test_bam_dedup.sorted.markdup.bam with duplicates marked2023-05-11 14:52:36,929 [ INFO] - Created output file test_bam_dedup.sorted.dedup.bam with duplicates removed
Robert Petkus 5/11/23