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User: Leonard Goldstein
Leonard Goldstein • 70
- Reputation:
- 70
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 3 months ago
- Joined:
- 4 years, 4 months ago
- Email:
- g*******@gene.com
Posts by Leonard Goldstein
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... There is no specific requirement for fragment or read length. I would follow standard recommendations for library preparation. The sequencing specs and read length sound fine.
...
written 3 months ago by
Leonard Goldstein • 70
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... Hi Andrea,
If you have the option to do strand-specific sequencing, this is still a good idea for transcriptome analysis (just not required for SGSeq). Read depth and replicates sound reasonable.
Best,
Leonard
...
written 3 months ago by
Leonard Goldstein • 70
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... Hi Andrea,
Actually strand-specific sequencing is not a requirement (the package was written a few years ago when most available data sets were not strand-specific). Since SGSeq relies on split reads, longer reads are helpful. There is no requirement for a particular sequencing depth. More reads a ...
written 3 months ago by
Leonard Goldstein • 70
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... exonsBy seems to be dropping a lot of genes, including MYC:
> tx <- makeTxDbFromBiomart()
> txs_by_gene <- transcriptsBy(tx, "gene")
> exs_by_gene <- exonsBy(tx, "gene")
> length(txs_by_gene)
[1] 63967
> length(exs_by_gene)
[1] 36751
> subsetByOverlaps(txs_by_gene, GRang ...
written 16 months ago by
Leonard Goldstein • 70
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... It looks like MYC is missing from the TxDb object you created, so this is a question about the makeTxDbFromBiomart function in the GenomicFeatures package. Maybe repost your question and add GenomicFeatures as one of the tags, and hopefully someone can help. Alternatively you can try using one of th ...
written 16 months ago by
Leonard Goldstein • 70
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... Hi Magda,
Can you please provide more details -- what commands were used to generate the SGFeatureCounts object and what package versions were used i.e. output of sessionInfo(). For larger analyses I strongly recommend not to use wrapper functions like analyzeFeatures() and instead run individual a ...
written 16 months ago by
Leonard Goldstein • 70
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Answer:
A: SGSeq error on getBamInfo
... The error message should list the problematic files but it returns an empty string. Looks like something went wrong that was not caught by the internal checks (probably unrelated to the XS tag). Are your BAM file paths correct and are index files present? You can try running the following and see if ...
written 16 months ago by
Leonard Goldstein • 70
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... Hi, since I can't reproduce the problem it is difficult to troubleshoot. As an alternative to TxDb objects, the convertToTxFeatures function also accepts a GRangesList of exons grouped by transcript. So you could try something like this
> tx <- exonsBy(hsaEnsembl, "tx", use.names = TRUE)
> ...
written 16 months ago by
Leonard Goldstein • 70
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... I could run this without any issues. If the problem persists maybe you can try reinstalling R and Bioconductor?
> library(GenomicFeatures)
> library(SGSeq)
> hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
> txf <- convertToTxFeatures(hsaEnsembl)
>
> se ...
written 17 months ago by
Leonard Goldstein • 70
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... Hi Sylvain,
Yes variantID() and eventID() are accessor functions for metadata columns in the SGVariant/Counts objects. You can see all available columns by typing mcols(sgv.counts). To extract gene names you can simply use geneNames(sgv.counts). Note this will return an empty CharacterList unless ...
written 18 months ago by
Leonard Goldstein • 70
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