Moderator: Rob

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Rob1.7k
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Posts by Rob

<prev • 142 results • page 1 of 15 • next >
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Answer: A: Effective length in normalisation for reads counts
... Methods that implement effective length correction all avoid generating negative effective lengths. Actually, they do this in quite a few different ways (depending on the tool). Actually, however, it might be most useful to think of the "effective length" as a property of both a transcript and a ...
written 8 days ago by Rob1.7k
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Comment: C: Converting TPM to FPKM
... Why would you do this, rather than converting FPKM to TPM? There is no benefit to FPKM over TPM and the FPKM to TPM conversion is trivial. ...
written 24 days ago by Rob1.7k
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Comment: C: Looking for advice on making a grad school decision on bioinformatics/computatio
... When I teach my grad class "Introduction to Computational Biology" (which is in our CS department), I actually try to de-emphasize the vague boundary between comp bio and bioinformatics. While many people, when asked, will define these slightly differently, I don't find there are useful canonical d ...
written 7 weeks ago by Rob1.7k
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Answer: A: Looking for advice on making a grad school decision on bioinformatics/computatio
... What type of work are you interested in? I spent a few years (as a postdoc) in the Comp Bio department at CMU (in Carl Kingsford's group). It's a fantastic department with (obviously) some really strong faculty and students. ...
written 8 weeks ago by Rob1.7k
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Comment: C: How is the FM-index built for multiple entries of a fasta file?
... Regarding your first question --- there are many different algorithms for generating the BWT+FM-index. Different tools will make use of different algorithms. One approach is to build the suffix array (again, there are many algorithms for this like DC3, and other suffix sorting algorithms; [this on ...
written 8 weeks ago by Rob1.7k
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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 8 weeks 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 8 weeks 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 9 weeks 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 11 weeks 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 3 months ago by Rob1.7k

Latest awards to Rob

Popular Question 1 day ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
Voter 5 days ago, voted more than 100 times.
Student 7 days ago, asked a question with at least 3 up-votes. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Great Question 11 days ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Appreciated 29 days ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 8 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Appreciated 3 months 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: Fast kmer reverse complement code using bit tricks
Popular Question 4 months ago, created a question with more than 1,000 views. For Comparing assembled transcripts against a reference
Popular Question 4 months ago, created a question with more than 1,000 views. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 4 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 7 months ago, created a question with more than 1,000 views. For Fragment Size: TLEN vs. isize
Appreciated 7 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 9 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 9 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
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
Good Answer 11 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 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

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