Moderator: Rob

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Rob2.0k
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@nomad421
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Posts by Rob

<prev • 150 results • page 1 of 15 • next >
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Answer: A: Mapping onto the Transcriptome, RNA-seq
... HISAT2 can probably be cajoled into aligning to the transcriptome directly, but it is designed to perform spliced read alignment to the genome directly. Bowtie2, on the other hand, is designed to map reads continuously to the indexed reference. It just happens to be particularly good at dealing wi ...
written 7 days ago by Rob2.0k
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Comment: C: salmon kallisto sleuth results in a genome browser ?
... Just for future reference, this can also be done with salmon using the [--writeMappings](http://salmon.readthedocs.io/en/latest/salmon.html#writemappings) flag. However, it's probably worth noting that the pseudo-SAM files produced by these programs are mapping records of fragments directly to the ...
written 10 days ago by Rob2.0k
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Answer: A: Reference for Salmon
... Yes, if you prepare a reference with rsem-prepare-reference it will work with salmon. ...
written 20 days ago by Rob2.0k
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Answer: A: Salmon libType is required but missing, although I thought I supplied it
... Hi Charles, The issue is that the libtype flag `-l` (short form) or `--libType` (long form) requires an argument. In your case, this would be `U` for unstranded. So, your full command would look like: `cm@node10:~/mouseRNAseq$ salmon quant -i mouseRNA_index -l U -r ./fastq/S1_R1.fastq.gz -p 8 ...
written 21 days ago by Rob2.0k
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Comment: C: tophat 2 rna seq
... Hi dimitrischat, It's worth noting that TopHat2 has been, essentially, [deprecated by the developers](https://ccb.jhu.edu/software/tophat/index.shtml), who recommend using HISAT2 instead. Unless you have a very specific reason to adopt TopHat2 in your pipeline, it's probably best to follow their ...
written 27 days ago by Rob2.0k
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Answer: A: Getting this message in SALMON's log file:""Greater than 5% of the fragments dis
... Hi biks.kestro, I just had a chance to respond to this on the salmon/sailfish user group [here](https://groups.google.com/d/msg/Sailfish-users/m1_vlC_jcu8/uJwBYPYIAwAJ). Please note that I moved your original post there since it was submitted as a response to our survey announcement rather than ...
written 28 days ago by Rob2.0k
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Answer: A: salmon, kallisto psuedoaligners are failing to process
... The issue is that you have samples where no reads are mapping. When there are no reads, there is no meaningful relative abundance of transcripts. I've recently (in the develop branch of salmon) changed the default behavior to be to warn the user and output a `quant.sf` file with all 0 TPMs. Howev ...
written 6 weeks ago by Rob2.0k
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Answer: A: combine or split, that's a question for transcriptome assembly
... By combining the samples prior to assembly, you increase the likelihood of generating (computationally) chimeric transcripts. You might try to assembly separately and then combine the assemblies using e.g. [TACO](https://tacorna.github.io). Also, TopHat has been deprecated by the developers. For ...
written 7 weeks ago by Rob2.0k
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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 weeks ago by Rob2.0k
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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 11 weeks ago by Rob2.0k

Latest awards to Rob

Commentator 10 days ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 15 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Scholar 19 days ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
Voter 8 weeks ago, voted more than 100 times.
Student 8 weeks ago, asked a question with at least 3 up-votes. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Great Question 9 weeks ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Appreciated 11 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
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 5 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Popular Question 5 months ago, created a question with more than 1,000 views. For Comparing assembled transcripts against a reference
Popular Question 6 months ago, created a question with more than 1,000 views. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 6 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 9 months ago, created a question with more than 1,000 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
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 10 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 11 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 11 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Appreciated 11 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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