User: Kathy

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Kathy0
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Posts by Kathy

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Comment: C: [diffbind] error when running dba.count
... Thank you. I posted at bioc site and the problem resolved. Here is the link https://support.bioconductor.org/p/126303/#126472 ...
written 17 days ago by Kathy0
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Answer: A: [diffbind] error when running dba.count
... I realized that those bgzf read were derived from bgzf.c (in htslib). Is there any way to avoid to run bgzf.c or htslib inside of dba.count()? Those 4 failed bam files were okay to run other program such as peak calling, etc. I wonder whether those errors not due to bam file itself. ...
written 23 days ago by Kathy0
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Comment: C: [diffbind] error when running dba.count
... They are paired ends, I used bowtie2. I've processed many other experiments using same workflow for diffbind. This is the first time I got this error. ...
written 28 days ago by Kathy0
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Comment: C: [diffbind] error when running dba.count
... That's what I thought as well. So I did re-run the parallel alignments for all the samples, and still 4 of 14 samples failed in diffbind dba.count() with the same error. I also did picard as you suggested, it seemed all the 14 samples got similar error as below (numbers vary) -- Error Type Count ...
written 28 days ago by Kathy0
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[diffbind] error when running dba.count
... I am running diffbind and has built up the dba object. When running dba.count(), there are few samples failed to process and encountered the following error message -- [W::bam_hdr_read] bgzf_check_EOF: No error [W::bam_hdr_read] bgzf_check_EOF: No error [E::bgzf_read] Read block operation failed ...
R chip-seq written 29 days ago by Kathy0

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