User: mbasam
mbasam • 0
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Posts by mbasam
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... 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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... 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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... 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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... 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 ...
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... Thank you for your valuable insight. The test worked. Best regards! ...
written 5 months ago by
mbasam • 0
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... 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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... 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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... 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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... 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 ...
written 5 months ago by
mbasam • 0
• updated
5 months ago by
Steve Lianoglou ♦ 12k
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