Moderator: Rob

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Rob2.3k
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2,340
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United States
Twitter:
@nomad421
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28 minutes ago
Joined:
7 years, 4 months ago
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Posts by Rob

<prev • 173 results • page 1 of 18 • next >
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Answer: A: CDS vs cDNA vs transcript for mapping RNA-Seq reads
... You should not map against the genome using Salmon. You can either download a transcriptome file, or a genome file and transcript annotations, and use a tool like gffread to extract the transcript sequences. You most likely want to quantify against the cDNA to account for features such as UTRs. ...
written 23 days ago by Rob2.3k
2
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1
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Answer: A: Library type warning in Salmon
... Hi Grant, Salmon's warnings are very conservative, in that it prefers to issue a warning to let you know that something _might_ be awry rather than letting potential issues go unnoticed. Specifically, with respect to the library strandedness, Salmon will issue a warning if >5% of the observed ...
written 5 weeks ago by Rob2.3k
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Answer: A: Number of threads in BWA
... Ok, as d-cameron points out below the situation I originally described is the case for Bowtie2, but not BWA. Apparently, BWA guarantees deterministic output order even when running concurrently with many threads (as Heng points out [here](https://www.biostars.org/p/116300/)). Thanks, d-cameron, fo ...
written 8 weeks ago by Rob2.3k
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Comment: C: How to find novel isoforms in RNA-Seq Data
... I'd add [scallop](https://github.com/Kingsford-Group/scallop) to that list of recent methods as well. ...
written 12 weeks ago by Rob2.3k
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Answer: A: Regarding GC correction in sequencing data
... Imagine that, due to GC bias, you are twice as likely to sample sequencing reads from a mid-GC region of the genome as a high-GC region of the genome. That is, all other things being equal (e.g. copy number), you will derive twice as many sequencing reads from mid-GC regions as from high-GC regions ...
written 5 months ago by Rob2.3k
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Answer: A: Hierarchical mapping of RNA-Seq data
... Hi Assa, I don't know of any tool that exactly does what you suggest. You might want to consider searching for "iterative alignment" or "iterative re-alignment", as searching the term "hierarchical mapping" in RNA-Seq will probably lead to a lot of hits for HISAT/HISAT2 (which is a great tool, ...
written 5 months ago by Rob2.3k
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Comment: C: TPM or FPKM as input values for PCA and WGCNA?
... [This blog post](http://blog.nextgenetics.net/?e=51) explains the issue nicely, with examples. ...
written 5 months ago by Rob2.3k
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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 6 months ago by Rob2.3k
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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 6 months ago by Rob2.3k
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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 months ago by Rob2.3k

Latest awards to Rob

Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 22 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Scholar 22 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Student 4 months ago, asked a question with at least 3 up-votes. For Fragment Size: TLEN vs. isize
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 6 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 8 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 8 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Great Question 8 months ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Popular Question 9 months ago, created a question with more than 1,000 views. For "Un-Projecting" genome alignments onto a transcriptome
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Popular Question 10 months ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 10 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Scholar 10 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 12 months ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
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Student 12 months ago, asked a question with at least 3 up-votes. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search

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