User: Anand Rao

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Anand Rao250
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Posts by Anand Rao

<prev • 157 results • page 1 of 16 • next >
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Comment: C: BBmap pipeline output varies across replicated runs
... Response from BBmap software author Brian Bushnell - at this SourceForge [link][1], and I quote him here: > I added a "seed" flag for the next release (30.71), which should make > the program deterministic. The default seed is -1, and negative seeds > will still produce nondeterminstic out ...
written 3 days ago by Anand Rao250
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... Oh OK, so HiSeq 2000 should not have optical duplicates, copy that. This means file before and after dedupe optical step should be (near) identical, correct ? This suggests there may be no value in this step for data generated on the HiSeq 2000 platform, correct? But performing it, would there be an ...
written 4 days ago by Anand Rao250
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Comment: C: BBmap pipeline output varies across replicated runs
... I'll keep that in mind, thanks Genomax. Just trying to make sure no one knocks me for non-reproducibility, and so I am checking that at each step in the pipeline. Perhaps that is overkill based on your experience... Thanks! ...
written 4 days ago by Anand Rao250
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... For **HiSeq 2000** platform, generating SE reads, is it still `dupedist=40` ? And for RNA-Seq data, we do not want to filter PCR duplicates, only the optical duplicates, correct? If so, the syntax for that would be, for SE reads, something like: clumpify.sh in=IN.fq.gz out=OUT_clumpd_dedupd.f ...
written 4 days ago by Anand Rao250
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Answer: A: BBmap pipeline output varies across replicated runs
... Here are my findings based on playing around with flags and trying to **reproduce** results: **1.** Variability in results from `filterbytile.sh` may be avoided with this flag during the run: `usekmers=f`. However, it is not entirely clear to me what circumstances allow versus disallow the use of t ...
written 18 days ago by Anand Rao250
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Comment: C: BBmap pipeline output varies across replicated runs
... I agree, the aligner should be able to take care of any bad reads in bad tiles. Pursuing my non-reproducibility of exact matched outputs for replicated runs, specifically for `filterbytile.sh`, I just found that using the following flag allows me to obtain reproducible results with: usekmers=f Th ...
written 21 days ago by Anand Rao250
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Comment: C: bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
... I agree, Michael. Here are my steps including and leading to the BBDUK decontamination step(s): rename.sh in=$IN out=$OUT fixsra=t -Xmx64g # from release 38.61, all other steps from release 38.60 IN=$OUT clumpify.sh -Xmx64g in=$IN out=$OUT dedupe optical IN=$OUT bbduk.sh -Xmx6 ...
written 23 days ago by Anand Rao250
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bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
... I seek help understanding these 2 flags for BBDUK of BBMAP = '**tossbrokenreads**' and '**nullifybrokenquality**' I see these flags mentioned in the STDERR of my **bbduk.sh step** using **BBMap version 38-60** while decontaminating Illumina SE 100nt raw reads via "Adapter and Quality Trimming" - pl ...
bbduk bbmap flags written 24 days ago by Anand Rao250 • updated 23 days ago by michael.ante3.5k
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Comment: C: BBmap pipeline output varies across replicated runs
... Genomax: Here is my 3 part update **PART 1** No problem with `rename.sh` step - gave matching results even previously /BBMap_38.61/bbmap/rename.sh in=SRR1726611.fastq out=SRR1726611_rename.fastq fixsra=t -Xmx20g # MATCHING RESULTS **PART 2** Your suggestion for seed=1 allowed me toreproduce ...
written 26 days ago by Anand Rao250
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Comment: C: BBmap pipeline output varies across replicated runs
... Hi genomax, Thanks for your super quick post. Yes, I am using as many threads as are available, which is usually 8 or 12 cores, each with 2 cpus (though my terminologies may be muddled, it is certainly > 1 core) For my step 1, `clumpify.sh` run I will try `seed = 1`, thanks for that suggestion ...
written 26 days ago by Anand Rao250

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