User: zhaolin20042008

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Posts by zhaolin20042008

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Comment: C: DiffBind: failed to run dba.count in SSH
... Many thanks.  1. I will update DIffBind 2.5.  2. Then I will change aligner bam file at the "bamReds" column. Z Zhang ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... Sorry for the late response. We are updating all the internet system within the department.  ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... > system("head 64502_macs2_peaks.narrowPeak") 1       10340   10634   64502_macs2_peak_1      59      .       4.99269 8.081125.94287  187 1       565190  565464  64502_macs2_peak_2      759     .       8.94809 79.14370         75.99088        155 1       566790  567199  64502_macs2_peak_3      80 ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... loaded via a namespace (and not attached):  [1] Rcpp_0.12.10            lattice_0.20-35         GO.db_3.2.2              [4] gtools_3.5.0            digest_0.6.12           plyr_1.8.4               [7] backports_1.0.5         futile.options_1.0.0    BatchJobs_1.6           [10] ShortRead_1.28.0     ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... > sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C           ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... It works when DBA was built but error stopped at dba.count(). I had ran the same script using R program in PC and it worked fine. However, short of memory space led me to follow the SSH linux system.  300073_57756 CD4 CLA Positive 0h 9 narrow 300073_57757 CD4 CLA Negative 0h 9 narrow 300073_57758 C ...
written 6 months ago by zhaolin200420080
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Comment: C: DiffBind: failed to run dba.count in SSH
... SampleID Tissue Factor Condition Treatment Replicate bamReads Peaks PeakCaller 4471_64502 CD4 CLA Positive 0h 1 64502_macs2_summits.bed  64502_macs2_peaks.narrowPeak  narrow 4471_64503 CD4 CLA Negative 0h 1 ...
written 6 months ago by zhaolin200420080
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DiffBind: failed to run dba.count in SSH
... Hi, I have tried to run R package- DiffBind in SSH (Linux). I have R script works will with windows R 3.3.3 but failed at SSH sever linux R. It stops at dba.count step. Could anyone help me? Does it mean the bam file is required instead of bed file?  Thank you.  #!/usr/bin/env Rscript args = comman ...
atac-seq ssh written 6 months ago by zhaolin200420080 • updated 6 months ago by Gord Brown540
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Answer: A: Error in lfproc(x, y, weights = weights, cens = cens,... : newsplit: out of ver
... I update my answer. I failed to change fitType in DiffBind as suggested. On the other hand, I changed the datasets in DBA project. Using plot(diff_count) and dba.plotPCA(diff_count,DBA_TREATMENT,label= DBA_ID), I could check the dataset distribution and relationship.Instead of a big DBA, I group the ...
written 7 months ago by zhaolin200420080
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DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
... Hi,  I got an error when I used DiffBind to treat a human ATAC-seq library data set. (see  https://support.bioconductor.org/p/94915/).ATAC-seq is the data set like DNase-seq, the enrichment of open chromatin region are variable.  Error in estimateDispersionsFit(object, fitType = fitType, quiet = ...
diffbind atac-seq written 7 months ago by zhaolin200420080

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