Moderator: Rob

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Rob2.2k
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Posts by Rob

<prev • 166 results • page 1 of 17 • next >
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Comment: C: Alignment dropped with Salmon
... Those defaults (k=19 for fmd and k=31 for quasi) are mentioned at the command line, but I'm not actually sure if they are in the documentation. We're preparing a new release, so I'll be sure to add them. ...
written 3 days ago by Rob2.2k
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Comment: C: Alignment dropped with Salmon
... The other big difference between these modes is the minimum size of an exact match that can be used by default. What is the length of your reads? You could also attempt building the default (quasi) index with a smaller k value. For example `-k 21` to see how that affects the mapping rate. ...
written 3 days ago by Rob2.2k
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Comment: C: Salmon very low mapping
... Hi Tania, Typically, you would simply include all of these RNAs in your index. In those samples where they are not present, Salmon will assign them an abundance of 0 (or very close to 0), but in those samples where you have a higher fraction of rRNA, they will show higher abundance. If you are ...
written 6 days ago by Rob2.2k
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Comment: C: Salmon very low mapping
... Hi Tania, Sure; let me try to describe it more completely. When you build a Salmon index, you construct it on some set of transcripts. That is, you obtain a fasta file of just transcript sequences using some tool like gff read or rsem-prepare-reference (along with a GTF and the genome), or, if ...
written 7 days ago by Rob2.2k
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Comment: C: Salmon very low mapping
... When you map the samples with TopHat, where are those reads that don't map with Salmon come from? You might consider including the rRNA sequences in the Salmon index you use to map the reads. ...
written 8 days ago by Rob2.2k
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Comment: C: Alignment dropped with Salmon
... As genomax mentions, if you map reads to the genome with a spliced mapper, but salmon doesnt map these reads to the transcriptome, tge big potential culprits are rRNA, intronic retention, or some other sort of genomic contamination. If it comes from an annotated transcript in the reference transcri ...
written 11 days ago by Rob2.2k
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Answer: A: From transcripts counts of Salmon to genes counts needed by edgeR
... The package [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html) provides an easy way to aggregate transcript level abundances to gene-level counts, and is likely the most popular approach in this kind of pipeline. *edit*: looks like Devon beat me to it by a few seconds ;P. ...
written 21 days ago by Rob2.2k
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Answer: A: Questions about Salmon
... Hi, Some thoughts related to your questions: > If one will probably map the reads in order to visualize downstream via tools like IGV, is it better to use the alignment based mapping so that Salmon agrees with the alignment output? Alignment-based Salmon deals with mappings of the reads agai ...
written 6 weeks ago by Rob2.2k
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Comment: C: How to calculate TPM of transcripts with isoforms
... That's correct. However, I'd still recommend using tximport if you're going to be using these estimates for anything other than visualization downstream, since it can correct for things that aren't possible to do looking at each sample in isolation (like the average expected gene length across all ...
written 6 weeks ago by Rob2.2k
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Answer: A: How to calculate TPM of transcripts with isoforms
... To aggregate abundance estimates to the gene-level, you should consider using a tool like [tximport](http://bioconductor.org/packages/release/bioc/html/tximport.html), and providing the transcript-to-gene mapping as input. Of course, the quality of the _de novo_ assembly can be a limiting factor in ...
written 6 weeks ago by Rob2.2k

Latest awards to Rob

Scholar 21 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
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Great Question 12 weeks ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
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Appreciated 6 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
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Scholar 9 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
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Popular Question 10 months ago, created a question with more than 1,000 views. For Comparing assembled transcripts against a reference
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