User: Leonard Goldstein

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Posts by Leonard Goldstein

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Answer: A: Extract sample information from own BAM files using SGSeq
... Please read the help page for getBamInfo and SGSeq vignette section 2. Note that your BAM files must contain the custom tag 'XS' for spliced reads. If you are looking for help with a particular problem or error you need to provide more information (error message, sessionInfo() output, aligner inform ...
written 8 days ago by Leonard Goldstein110
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Comment: C: Custom gene annotations for SGSeq
... You can add junctions manually for a TxFeatures object. But you have to be careful that coordinates are consistent with exons. Junction starts and ends have to coincide with exon ends and start, respectively. Here is an example for TxFeatures object txf_ann that comes with the package: new_junc ...
written 16 days ago by Leonard Goldstein110
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Answer: A: Custom gene annotations for SGSeq
... Yes you can work with a combination of annotated and predicted gene models. The easiest way to do this is to use analyzeFeatures() for annotated gene models as explained in the vignette but with predict = TRUE. ...
written 16 days ago by Leonard Goldstein110
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Comment: C: using only uniquely-mapping reads for alternative splicing using SGSeq
... Actually looking at the code in more detail, BamFile details from the sample information currently do not propagate. The hard-coded behavior is that only primary alignments in the BAM file are considered for analysis. In other words, each read should be analyzed only once, but the analysis may inclu ...
written 8 weeks ago by Leonard Goldstein110
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Answer: A: using only uniquely-mapping reads for alternative splicing using SGSeq
... You can influence which reads are analyzed when setting up the data frame with sample information. To do this column file_bam needs to be a BamFileList and sample information must be stored in a DataFrame object. Please see the manual page for Rsamtools::BamFileList for more details. ...
written 8 weeks ago by Leonard Goldstein110
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Comment: C: I can't import my gff file by `importTransprits()`,when I worked with SGSeq.
... Both are possible. Please see vignette section 6 for an example on how to analyze a particular region of the genome using the `which` argument. If no region is specified the analysis is genome-wide. Depending on your data set, genome-wide predictions can be computationally intensive. In case you run ...
written 8 months ago by Leonard Goldstein110
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Answer: A: I can't import my gff file by `importTransprits()`,when I worked with SGSeq.
... When posting a question about a software package, please always tag your post with the package name. This triggers an automatic email from the system to the package maintainer. Regarding your question -- the `tag_tx` and `tag_gene` arguments are for specifying names of the relevant GFF tags. Pleas ...
written 8 months ago by Leonard Goldstein110
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Comment: C: Which sequencing parameters are required for SGSeq analysis of splice events?
... 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 13 months ago by Leonard Goldstein110
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Answer: A: Which sequencing parameters are required for SGSeq analysis of splice events?
... 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 13 months ago by Leonard Goldstein110
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Answer: A: Which sequencing parameters are required for SGSeq analysis of splice events?
... 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 13 months ago by Leonard Goldstein110

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