User: Fei Liu

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Fei Liu0
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Posts by Fei Liu

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Error in running ATACseqQC
... After testing, the splitGAlignmentByCut function may depend on the shiftGAlignmentsList function and use the same parameters, so I obtained adapt output successfully. But splitBam function still not work. Thank you all. ...
written 29 days ago by Fei Liu0
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Comment: C: Error in running ATACseqQC
... And I try to use bowtie2 to get sam file, then samtools and try splitBam function again, there also have some error. > objs <- splitBam(bamfile,tags=tags,outPath='/simm/huangyulab/liufei/Owl/bowtie2_build_ref/split_1Bam',txs=txs,genome=Hsapiens,conservation=phastCons100way.UCSC.hg19) ...
written 4 weeks ago by Fei Liu0
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Comment: C: Error in running ATACseqQC
... Thanks for your reply. The command pdf(file=xxx.pdf .....) not work, although that produce a new pdf, it can not open to watch. I tried the example code successfully, and to I downloaded the SRR891280 [https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR891280][1] and tried again, but also got the s ...
written 4 weeks ago by Fei Liu0
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Comment: C: Error in running ATACseqQC
... sessionInfo R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so ...
written 4 weeks ago by Fei Liu0
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Error in running ATACseqQC
... There are some issues when running **ATACseqQC**. 1. In out-pdf functions such as fragSizeDist, PTscore, only when I exit R session can I get non-empty pdf document, and if I don't exit R, the out-pdf is always empty, so that run a function, I have to go into R, and then exit to get the target file ...
software error written 5 weeks ago by Fei Liu0
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Comment: C: How could I get index file
... Thank you for the prompt answer. ...
written 6 weeks ago by Fei Liu0
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How could I get index file
... Hi all, I'm trying to test ATAC-seq data through ATACseqQC, first download SRR891278, which then transfer to sam file use bwa mem, and then tranfer to bam file use samtools view and samtools sort, but get an error below. > bamfile <- '/simm/huangyulab/liufei/test/atac-testdata/SRR891278. ...
go written 6 weeks ago by Fei Liu0 • updated 6 weeks ago by Martin Morgan ♦♦ 24k

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