User: tomas.rodriguez

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Posts by tomas.rodriguez

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GUIDEseq Error in GAlignmentPairs
... I'm not sure why one set of bam files in my dataset is producing the below error. To be safe, I re-trimmed and re-aligned my fastqs and got the same result. Is this something I can suppress somehow? This can't possibly mean length of the bams because all of my bams have a different number of lines a ...
galignmentpairs guideseq written 7 weeks ago by tomas.rodriguez0 • updated 6 weeks ago by Julie Zhu4.0k
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GUIDEseq outputDir error
... Hi Julie, Given the below input, GUIDEseqAnalysis(outputDir) only stores "PlusMinusPeaksMerged.xls" and "offTargetsInPeakRegions.xls" in the specified directory. "#name#bamReadSummary.xls" and "#name#PlusMinusPeaksMerged.bed" are stored in the working directory. Is this intentional? guideSeqResult ...
guideseq written 8 weeks ago by tomas.rodriguez0 • updated 8 weeks ago by Julie Zhu4.0k
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Comment: C: GUIDEseq plus/minus strand inputs
... Hi Julie, Thanks for your reply. As far as I know, GUIDEseq samples are typically sequenced using this configuration: 150/8/16/150 R1/Index1/Index2/R2 where Index 1 and 2 are the i7 and i5 sides, respectively. It appears that binReads.sh, getBarcode.pl and getUMI.pl do no read standard sequencing ...
written 8 weeks ago by tomas.rodriguez0
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GUIDEseq plus/minus strand inputs
... What file(s) are required as input for alignment.inputfile? I see several references to varibles "extdata" and "alignFile" in the documentation, but little explanation as to how these files are handled. If a sequencing run is not compatible with binReads.sh (and/or getBarcode.pl), the user has littl ...
guideseq written 8 weeks ago by tomas.rodriguez0 • updated 8 weeks ago by Julie Zhu4.0k
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GUIDEseq bam input
... I cannot find any explicit requirement for sorted bam files in the manual, but they are carry a "sort" extension in the vignettes. Is sorting required? ...
bam guideseq written 8 weeks ago by tomas.rodriguez0 • updated 8 weeks ago by Julie Zhu4.0k

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