Moderator: Rob

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Rob2.1k
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Posts by Rob

<prev • 155 results • page 1 of 16 • next >
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Answer: A: Convert a FASTA Amino Acid Sequence to RNA (Reverse Central Dogma)
... The key point you should note here is that a given codon implies a single amino acid, but a particular amino acid could result from multiple different codons. The reverse operation does not have a unique solution. Consider an amino acid sequence a_1, a_2, ..., a_n, where c_1, c_2, ..., c_n are the ...
written 1 day ago by Rob2.1k
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Answer: A: Salmon TPMs not the same for each strand individually (--libType IU)?
... Hi brismiller, This is actually not _too_ surprising. Specifically, what you're losing in this case is the actual pairing information. Often, a pair of reads is more informative than either of the individual reads, and so the read pair maps to a more restrictive set of transcripts, and hence le ...
written 12 days ago by Rob2.1k
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Answer: A: TPM VS FPKM VS TMM and K-mer specific expression quantification
... To add to h.mon's answer, there is generally no "absolute" measurement for transcript expression. For example, the number of reads assigned to each transcript depends on sampling depth, relative abundnaces, etc. I have written a blog post on some of the different expression measurements that are com ...
written 7 weeks ago by Rob2.1k
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Comment: C: Reference for Salmon
... Users have had success using salmon for such quantification tasks before. So, if you provide it with the proper reference, yes; it should work as well as RSEM for this task. ...
written 8 weeks ago by Rob2.1k
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Comment: C: Reference for Salmon
... I generally like the [GenCode reference](ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.transcripts.fa.gz), since it's fairly comprehensive and you can get the sequences directly (rather than having to build them from the genome + gtf). You can [also get just the protein-co ...
written 8 weeks ago by Rob2.1k
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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 10 weeks ago by Rob2.1k
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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 weeks ago by Rob2.1k
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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 12 weeks ago by Rob2.1k
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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 12 weeks ago by Rob2.1k
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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 3 months ago by Rob2.1k

Latest awards to Rob

Appreciated 1 day ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 1 day ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Good Answer 1 day 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 1 day ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Great Question 23 days ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Popular Question 4 weeks ago, created a question with more than 1,000 views. For "Un-Projecting" genome alignments onto a transcriptome
Good Answer 6 weeks 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 8 weeks ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Scholar 11 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 11 weeks ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Popular Question 3 months ago, created a question with more than 1,000 views. For Perplexing Bowtie 2 results
Voter 4 months ago, voted more than 100 times.
Student 4 months ago, asked a question with at least 3 up-votes. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Great Question 4 months ago, created a question with more than 5,000 views. For Fragment Size: TLEN vs. isize
Appreciated 4 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
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
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 Comparing assembled transcripts against a reference
Popular Question 8 months ago, created a question with more than 1,000 views. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Fast kmer reverse complement code using bit tricks
Scholar 8 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data

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