User: mbasam

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Posts by mbasam

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Comment: C: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you? ...
written 4 months ago by mbasam • 0
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Comment: C: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you? ...
written 4 months ago by mbasam • 0
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Comment: C: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... Hi Julie, I have the most recent version of ATACseqQC (1.8.1) installed. Here is the session info: R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /opt/R/3.6.0-Python-3.6.6-foss-2018b/lib64/R/lib/libRblas.s ...
written 5 months ago by mbasam • 0
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ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... When trying to use ATACseqQC on a larger bamfile, I receive the following error: **Error in .local(x, ...) : strand values must be in '+' '-' '*' Calls: splitGAlignmentsByCut ... normalize_strand_replacement_value -> strand -> strand -> .local** I checked the structure of the bamfile usi ...
R atacseqqc written 5 months ago by mbasam • 0 • updated 5 months ago by Julie Zhu • 4.1k
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Comment: C: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
... Thank you for your valuable insight. The test worked. Best regards! ...
written 5 months ago by mbasam • 0
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Comment: C: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
... Hi Jianhong, Here is the filter code: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R And here is subset of the bam file: http://s3.amazonaws.com/mudaser/bamfiles/chr21-filt.bam ...
written 5 months ago by mbasam • 0
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Comment: C: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
... Hi Jianhong, Here is the filter code: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R And here is subset of the bam file: http://s3.amazonaws.com/mudaser/bamfiles/chr21-filt.bam ...
written 5 months ago by mbasam • 0
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Comment: C: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
... Hi Jianhong, How can I send you these files and code? Can please provide me with an email address so that I could send you a link to the file and code? ...
written 5 months ago by mbasam • 0
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
... All other parts of the ATACseqQC package works, but when the shiftGAlignmentsList command is ran to shift the reads and split the BAM files, the command fails with the following error: (all(elementNROWS)>3) is not TRUE. However, in R, when I run that line, it returns as TRUE. What is the exact er ...
software error atac tutorial atacseqqc atacseq written 5 months ago by mbasam • 0 • updated 5 months ago by Steve Lianoglou ♦ 12k

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