User: Leonard Goldstein

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Posts by Leonard Goldstein

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Error when predicting features with SGSeq
... Hi Helen, If it is an option to make available the current BAM files, I can have a look at the data to understand what is causing the problem.  Otherwise I suggest running SGSeq on the unmodified TopHat output when you get the chance and if you are still encountering problems, please do report the ...
written 4.1 years ago by Leonard Goldstein80
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Answer: A: Error when predicting features with SGSeq
... Hi Helen, Thanks for providing the sessionInfo output.  It sounds like these are non-standard BAM files (merged from different sources). Can you try running SGSeq on the unmodified BAM files that were generated by TopHat?  Leonard   ...
written 4.1 years ago by Leonard Goldstein80
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Answer: A: Error when predicting features with SGSeq
... Hi Helen, Thanks for your question. Can I ask what version of SGSeq you are using? The output of sessionInfo() would be helpful. BAM files used as input for SGSeq should be RNA-seq data mapped to a reference genome with a splice-aware aligner that includes the custom tag XS in the BAM output (e.g. ...
written 4.1 years ago by Leonard Goldstein80
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Comment: C: performance issues when using readGAlignmentPairs with a ‘which’ argument
... OK thanks for the clarification! ...
written 4.5 years ago by Leonard Goldstein80
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Answer: A: performance issues when using readGAlignmentPairs with a ‘which’ argument
... Hi Martin, many thanks for fixing this. Regarding the discordant alignments - I assume flag bit 0x2 was used to assess whether reads are properly paired? Seems like definition of “properly paired” is aligner-specific, e.g. for GSNAP properly paired does not imply that paired alignments are in the ex ...
written 4.5 years ago by Leonard Goldstein80
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Comment: C: performance issues when using readGAlignmentPairs with a ‘which’ argument
... OK thanks for sending the temporary workarounds. ...
written 4.5 years ago by Leonard Goldstein80
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Answer: A: performance issues when using readGAlignmentPairs with a ‘which’ argument
... Hi Hervé, Thanks for the quick reply. Yes I run into the same problem when using scanBam, as suggested. Thanks for looking into this. Leonard ...
written 4.5 years ago by Leonard Goldstein80
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performance issues when using readGAlignmentPairs with a ‘which’ argument
... Hi all, I ran into performance issues when using readGAlignmentPairs with a ‘which’ argument (passed via a ScanBamParam object). I’m working with a BAM file with paired alignments that can be read with readGAlignmentPairs in ~15 minutes. The function call results in a warning message regarding 30 ...
genomicalignments written 4.5 years ago by Leonard Goldstein80
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Answer: A: SGSeq error on analyzeFeatures
... Hi Paolo, I haven’t used STAR myself but the manual suggests there is an option that allows STAR to generate the XS tag. See section 4.2.2. SAM attributes and 4.2.3 Compatibility with Cufflinks/Cuffdiff in the STAR manual 2.4.0.1. I will need to clarify the XS tag requirement in the documentation ...
written 4.7 years ago by Leonard Goldstein80
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Answer: A: SGSeq error on analyzeFeatures
... Hi Paolo, Thanks for providing your code and test files. It looks like the problem is caused by missing information in the BAM files.  Firstly, you mentioned the data are paired-end. However, your BAM files look like reads were aligned as single-end data. There is a recent post on the Bioconductor ...
written 4.7 years ago by Leonard Goldstein80

Latest awards to Leonard Goldstein

Popular Question 4.1 years ago, created a question with more than 1,000 views. For performance issues when using readGAlignmentPairs with a ‘which’ argument
Popular Question 4.1 years ago, created a question with more than 1,000 views. For GenomicRanges flank function with ignore.strand=TRUE
Popular Question 4.1 years ago, created a question with more than 1,000 views. For GRangesList mcols names

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