User: Shuang He

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Shuang He0
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Posts by Shuang He

<prev • 8 results • page 1 of 1 • next >
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ATAC-QC shiftGAlignmentsList function
... I tried to use ATAC-QC to generate the ATAC-seq QC plots , but I met some problem with the shiftGAlignmentsList function. Thank you for your help in advance. ``` bamfile <- "G:/project/ATAC-seq_QC/rdrmbam/my.rdrm.bam" possibleTag <- combn(LETTERS, 2) possibleTag <- c(paste0(pos ...
atac-seq atacseqqc written 5 weeks ago by Shuang He0 • updated 4 weeks ago by Julie Zhu4.0k
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ATAC-QC fragSizeDist function
... I tried ATAC-QC package For the fragSizeDist function, I wonder that whether the input bam file need to be the raw bam files which include the chrM, duplicates. When I tried to input the bam file (q30) which was removed the adapters,duplicates, chrM, the fragment distribution seemed a little strang ...
atac-seq atacseqqc written 5 weeks ago by Shuang He0 • updated 5 weeks ago by Julie Zhu4.0k
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Comment: C: DESeq2 for Cut&Run and differential enrichment testing
... Hi, I have a question which is not related with your question. I wonder what do you mean "normalize the data to the number of mapped reads generated from S.cerevisiae spike-in"?   Did you divide the ChIP read count by the corresponding spike in mapped reads? ...
written 8 months ago by Shuang He0
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Comment: C: Rsamtools undefined symbol: gzopen64
... Thank you very much.Yes,I contacted system administrator.And I replaced PKG_LIBS = ${PKG_LIBS0} /lib64/libz.so.1.2.11 with PKG_LIBS = ${PKG_LIBS0} /usr/local/lib/libz.a (or with -L ) but both  doesn't work . $/path/R-3.5.1/bin/R CMD INSTALL Rsamtools * installing to library ‘/path/R-3.5. ...
written 12 months ago by Shuang He0
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Comment: C: Rsamtools undefined symbol: gzopen64
... Thanks again. but now it reported new errors after updating. ** testing if installed package can be loaded Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/path/R-3.5.1/library/Rsamtools/libs/Rsamtools.so': /lib64/l ...
written 12 months ago by Shuang He0
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Comment: C: Rsamtools undefined symbol: gzopen64
... Thanks,Martin.But after editing the  Rsamtools/src/Makevars(simply use vim), I still got the same errors. Following is the whole Rsamtools/src/Makevars file:  include Makevars.common PKG_CFLAGS = ${PKG_CFLAGS0} PKG_LIBS = ${PKG_LIBS0} -lz PKG_LIBS = ${PKG_LIBS0} -L/lib64/libz.so.1.2.11 libs0: ...
written 12 months ago by Shuang He0
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Rsamtools undefined symbol: gzopen64
... Hi,when I tried to install Rsamtools ,I get the errors: Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/lustre1/cxu_pkuhpc/program/R-3.5.1/library/Rsamtools/libs/Rsamtools.so':   /path/R-3.5.1/library/Rsamtools/libs/ ...
rsamtools gzopen64 zlib written 12 months ago by Shuang He0 • updated 12 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Rsamtools installation error
... Hi,I came across the same problem and I followed the steps that you discussed . $/lustre1/cxu_pkuhpc/program/R-3.5.1/bin/R CMD ldd Rsamtools/src/Rsamtools.so     linux-vdso.so.1 (0x00007fffec7ff000)     libz.so.1 => /lib64/libz.so.1 (0x00002b4ce4d61000)     libstdc++.so.6 => /usr/lib64/lib ...
written 12 months ago by Shuang He0

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