Moderator: Rob

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Rob1.7k
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Posts by Rob

<prev • 137 results • page 1 of 14 • next >
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Comment: C: More specifics on Jellyfish -C methodology.
... According to the jellyfish manual (https://github.com/gmarcais/Jellyfish/blob/master/doc/jellyfish.pdf) "whichever comes first lexicographically". So, in your case, it would be `ATG> 5`. ...
written 2 days ago by Rob1.7k
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Answer: A: More specifics on Jellyfish -C methodology.
... There is no special accounting for paired end reads in Jellyfish (or any kmer counting software of which I'm aware). The -C option just means that when Jellyfish looks at a kmer k, it considers both k and rc(k). It associates k and rc(k) with whichever of the two is alphabetically smaller. This m ...
written 2 days ago by Rob1.7k
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Answer: A: How is the FM-index built for multiple entries of a fasta file?
... Hi yifangt86, There are a few ways to go about building a multi-string BWT. Perhaps the simplest is the following. Consider a collection of N original strings, S1, S2, ... SN. Now, form a new string S = S1$S2$...$SN (you can use any separator that is a character that doesn't appear in the tex ...
written 5 days ago by Rob1.7k
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Answer: A: Correct for GC content bias RNASeq DE
... Hi /u/debitboro, One of the main technical issues with GC bias in RNA-seq data is that there can be sample-specific, fragment-level GC bias. That is, the probability of sampling a particular fragment (i.e, paired-end read) can depend upon the GC content of that fragment (see the excellent blog p ...
written 18 days ago by Rob1.7k
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Comment: C: Main difference between RSEM and k-mer based quantification methods
... Just to comment a bit on Devon's (accurate & ideal) response. We've actually been looking into the fine-grained particulars of this and have a paper under submission that explores the nature of the small differences in some detail. There are at least two potential reasons for the differences o ...
written 5 weeks ago by Rob1.7k
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Comment: C: Differences between Counts and FPKMS
... True, but spike-ins can exhibit crazy variability / imprecision. Theoretically they are great, but their practical utility is mediated to a large degree by the skills of the person preparing the samples. ...
written 5 weeks ago by Rob1.7k
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Comment: C: Differences between Counts and FPKMS
... agreed with the agreement ;P. I'd only offer the caveat that, while TPM is universally preferable to F/RPKM, it is still a purely relative abundance metric. For this reason alone, it's not really appropriate to use as is for quantitative comparison between samples / condition . ...
written 5 weeks ago by Rob1.7k
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Comment: C: Differences between Counts and FPKMS
... Don't use fold changes from FPKM for any type of quantitative analysis. They will not be properly normalized for comparisons between samples or replicates. You should instead look at fold changes that normalize for these differences. In a "standard" analysis, DESeq / DESeq2 / EdgeR / limma will p ...
written 5 weeks ago by Rob1.7k
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Answer: A: Differences between Counts and FPKMS
... Hi Ron, These are completely different measures. As mforde84 points out, raw read counts don't normalize for (1) the fact that a transcript / gene will produce counts that depend on the gene's length and (2) the fact that, in different samples, a particular read count may have different meanings ...
written 5 weeks ago by Rob1.7k
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Answer: A: Shortest Missing K-mer
... I think the question is not particularly well-posed. That is "what do you expect is the length of the shortest missing k-mer in the genome (i.e. it does not appear)?" depends on how I define my expectation of missing. However, one reasonable interpretation would be the following. I expect a k-mer ...
written 6 weeks ago by Rob1.7k

Latest awards to Rob

Scholar 2 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 5 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Comparing assembled transcripts against a reference
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 12 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 5 months ago, created a question with more than 1,000 views. 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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Good Answer 7 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....
Appreciated 7 months ago, created a post with more than 5 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Appreciated 8 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
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....
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Popular Question 10 months ago, created a question with more than 1,000 views. For Sequence Evolution Library In Java
Scholar 12 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
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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