Moderator: Rob

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Rob2.2k
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@nomad421
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Posts by Rob

<prev • 169 results • page 1 of 17 • next >
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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 8 weeks ago by Rob2.2k
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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 10 weeks ago by Rob2.2k
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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 10 weeks ago by Rob2.2k
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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 months 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 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by Rob2.2k

Latest awards to Rob

Student 5 weeks ago, asked a question with at least 3 up-votes. For Fragment Size: TLEN vs. isize
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 3 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Good Answer 5 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....
Scholar 5 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Great Question 5 months ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Popular Question 5 months ago, created a question with more than 1,000 views. For "Un-Projecting" genome alignments onto a transcriptome
Good Answer 6 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 6 months ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 7 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Scholar 7 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
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Student 9 months ago, asked a question with at least 3 up-votes. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Great Question 9 months ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Appreciated 9 months ago, created a post with more than 5 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
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 12 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data

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