Moderator: Rob

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Rob3.0k
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Posts by Rob

<prev • 207 results • page 1 of 21 • next >
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Answer: C: RNA-Seq:How to know RNA-seq data is Strand-Specific or not based on only fastq
... If you simply quantify the data with `salmon` using library type `-l A`, it will infer the most likely library format (stranded vs. unstranded) for you. ...
written 11 days ago by Rob3.0k • updated 11 days ago by ATpoint12k
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Answer: A: How to change cellranger multimapping algorithm
... The cellranger UMI deduplication algorithm does not handle reads that map among multiple genes, there is no "easy" way to handle this situation. You may be interested in taking a look at our quantification tool, [alevin](https://www.biorxiv.org/content/early/2018/10/24/335000), which we've designed ...
written 15 days ago by Rob3.0k
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Answer: A: Average Insert Size When Using Transcript Quantification Tools Such as Salmon?
... Is the data paired-end? In this case, salmon estimated the fragment length distribution. In the quantification directory the file `libParams/flenDist.txt` contains the parameters of the normalized distribution of observed fragment lengths. Each of the 1001 numbers gives the probability of observi ...
written 12 weeks ago by Rob3.0k
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Comment: C: best pipeline to get gene and transcript counts
... You can reduce the memory required by star by building the index with the `--genomeSAsparseD` parameter set to a value greater than 1. This samples the suffix array. If the value is too large, STAR will become slower, but small values (e.g. 2/4) can provide a nice memory savings without slowing th ...
written 3 months ago by Rob3.0k
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Comment: C: best pipeline to get gene and transcript counts
... No. STAR has the ability to perform a single alignment against genome (and gtf), and to provide 2 separate outputs using the same alignments. One BAM file contains the spliced alignments to the genome. The other BAM file contains the unspliced alignments to the transcriptome (suitable to provide ...
written 3 months ago by Rob3.0k
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Comment: C: best pipeline to get gene and transcript counts
... In this case, as I suggested, the easiest path is to align with STAR and keep both the genome alignments and get the transcriptome alignments. As swbarnes2 mentions below, you can even use STARs `--quantMode` for the genome-level counts. Note, however, that you won't be able to get transcript leve ...
written 3 months ago by Rob3.0k
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Comment: C: best pipeline to get gene and transcript counts
... I see. In that case, perhaps consider aligning with STAR, which can give you both the genome and transcriptome alignments at the same time. The genome alignments can be counted using featureCounts, and the transcriptome alignments can be fed to salmon for transcript-level quantification. Also, it ...
written 3 months ago by Rob3.0k
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Comment: C: best pipeline to get gene and transcript counts
... Did you align against the genome or transcriptome? If you want to use a traditional aligner to provide input to salmon (rather than using its builtin mapping algorithm), then you should either (1) align to the genome with STAR and tell it to project the alignments to the transcriptome (it can do th ...
written 3 months ago by Rob3.0k
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... The effect of the `--geneMap` flag is to cause salmon to output, in addition to it's transcript level quantifications, aggregated gene-level quantifications. However, this flag exists only for backward compatibility and is deprecated in favor of tximport. Though it attempts to do the same thing, t ...
written 3 months ago by Rob3.0k
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... I'd recommend going with the quasi-mapping, and including the `--validateMappings` option among your command line flags (including others that seem relevant for your data given the documentation). ...
written 3 months ago by Rob3.0k

Latest awards to Rob

Scholar 19 hours ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Good Answer 9 days 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 11 days ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Appreciated 9 weeks ago, created a post with more than 5 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: Can pairwise global alignment be done in linear memory with affine gap penalties
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Good Answer 11 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....
Scholar 3 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Scholar 4 months ago, created an answer that has been accepted. For A: Estimating RPKM or TPM in RNA-Seq data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Teacher 5 months ago, created an answer with at least 3 up-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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: best workflow for RNA data analysis without replications
Popular Question 6 months ago, created a question with more than 1,000 views. For "Un-Projecting" genome alignments onto a transcriptome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
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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