Moderator: Rob

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Rob3.7k
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@nomad421
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9 years, 2 months ago
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Posts by Rob

<prev • 237 results • page 1 of 24 • next >
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Comment: C: hisat2 salmon alignment error
... No, this will simply prevent HISAT2 from aligning reads outside of annotated transcripts. These will still be spliced alignments in genomic coordinates. As far as I know, HISAT2 has no option to project genomic alignments to transcriptomic coordinates, so the only way to accomplish this with HISAT ...
written 8 days ago by Rob3.7k
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Answer: A: hisat2 salmon alignment error
... You aligned your reads to the *genome* with HISAT2, and you are trying to quantify the transcriptome with salmon. The references are not the same, and salmon does not (currently) support consuming genome-aligned BAM files for transcriptome quantification. You either need to align the reads directl ...
written 8 days ago by Rob3.7k
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Comment: C: parameters mapping in salmon software
... If you have access to the quantification directories output by salmon, then, within each directory, the `cmd_info.json` file encodes the precise command line parameters passed to salmon that generated the quantification results. Again (and as @genomax denotes above), default parameters are often im ...
written 14 days ago by Rob3.7k
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Comment: C: parameters mapping in salmon software
... I would recommend you state in your manuscript the specific version of the software you used, as well as all relevant parameters you passed via the command line. You should ideally do this for all the software tools you used in your paper. However, it is not typical (or reasonable) for a reviewer ...
written 15 days ago by Rob3.7k
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Comment: C: can salmon distinguish similar transcript?
... By default, the mapping information is not written out. If you run salmon with the `--writeMappings` flag, and give it a file to write the mappings to, then it will write a SAM file with the mappings it generated. ...
written 4 weeks ago by Rob3.7k
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Answer: C: can salmon distinguish similar transcript?
... Yes; in general the ability to distinguish between similar transcripts should be quite good. Of course, it depends on the exact read evidence. If the reads deriving from these transcripts overlap very few (or no) variants, then there is no specific evidence of the presence of one transcript versus ...
written 4 weeks ago by Rob3.7k
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Answer: A: warning when creating salmon index from GENCODE transcriptome
... The reason salmon gives this message is because the Gencode transcripts have (for the purposes most people want to use them for) unnecessarily long and convoluted names. Specifically, there is the transcript id, and then a considerable amount of metadata encoded in the record name, separated by `|` ...
written 5 weeks ago by Rob3.7k
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Comment: C: Salmon only processes human reads from PDX data
... Hi jrleary, I don't have an answer for this, but I can say that `Run human only on original .fasta` is not an error message generated by salmon itself. Are there some extra checks that happen when you submit your job? ...
written 9 weeks ago by Rob3.7k
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Comment: C: Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis
... Hello harshraje19! Questions similar to yours can already be found at: Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why ...
written 3 months ago by Rob3.7k
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Comment: C: Issue with index creation in RapMap
... It looks as though the index is being created properly. What is the output of the mapping phase? Have you looked at all at the SAM file being produced? Does that contain records that look like valid mappings? ...
written 3 months ago by Rob3.7k

Latest awards to Rob

Scholar 5 weeks ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Good Answer 4 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....
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Student 5 months ago, asked a question with at least 3 up-votes. For Comparing assembled transcripts against a reference
Scholar 6 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties
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....
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
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....
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: How to handle Reverse complement in De-Bruijn Graph
Epic Question 8 months ago, created a question with more than 10,000 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 11 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
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: How to handle Reverse complement in De-Bruijn Graph
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 13 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties

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