User: molly_the_minotaur

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Posts by molly_the_minotaur

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Comment: C: ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is I
... Hi Tom,  Could you post the potential reason for why dup% is 0? My input files are BAM files. Both QC report from before and after I performed the deduplication using fastx_collapser from FASTX-Toolkit showed the same results.  Thanks! ...
written 5 weeks ago by molly_the_minotaur20
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Comment: C: ChIPQC - can't read in bam files
... I can't get the ChIPQC installed on the server R 3.5 because anaconda conflicts. There are many dependencies couldn't be installed. Do you think the errors in this post are due to the older R version 3.4.1?    ...
written 9 weeks ago by molly_the_minotaur20
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Comment: C: ChIPQC - can't read in bam files
... I do have the index files (.bai) under the same folder. I have R 3.5 installed on a server that I’ll test the same function again this afternoon. Thanks for the suggestion  @James  ...
written 9 weeks ago by molly_the_minotaur20
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ChIPQC - can't read in bam files
...     Having trouble to get the ChIPQC to work properly. My ultimate goal is to have the html report generated using ChIPQCreport(). I read in the bam files through dba function in the DiffBind package. All went well and I was able to run all DiffBind functions. Using the same sample sheet and dba ...
chipqc chipqcreport written 9 weeks ago by molly_the_minotaur20

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