User: Anand Rao

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Anand Rao280
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Posts by Anand Rao

<prev • 160 results • page 1 of 16 • next >
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Answer: A: rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
... After much discussion with the Ram team, specifically Eric Nawrocki, one of the Infernal software suite's authors, the covariance models (CMs) in Rfam for rRNA sequences are built from the maximum possible breadth of taxonomic range. As a result, some regions of the CMs are not as conserved as they ...
written 2 days ago by Anand Rao280
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Comment: C: rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
... Hi [Brian][1], [Genomax][2], et al., With help from Rfam team, I was able to detect four group II introns, in 3 out of 62 [rRNA gene sequences][3], as matches to [RF00029][4], using [Infernal][5] suite's cmscan on the command line, with syntax similar to the example at this Rfam [weblink][6]. So s ...
written 9 weeks ago by Anand Rao280
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rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
... Greetings! I need some help with performing my rRNA decontamination step properly, which is part of pre-processing pipeline for my Illumina RNA-Seq reads, before mapping to the reference genome (a plant species). **SOME RELEVANT LINKS AND MY CRUDE INFERENCES**: https://www.biostars.org/p/65793/ - ...
rrna sormerna intron bbsuite rna-seq written 12 weeks ago by Anand Rao280
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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 months ago by Anand Rao280
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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 3 months ago by Anand Rao280
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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 3 months ago by Anand Rao280
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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 3 months ago by Anand Rao280
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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 4 months ago by Anand Rao280
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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 4 months ago by Anand Rao280
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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 4 months ago by Anand Rao280

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