User: Wang

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Wang0
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Posts by Wang

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Comment: C: Why ranges of narrowPeak file and that of bed file are not identical
... OK,thank you.May be I missed some useful information.I'll read these again. ...
written 15 days ago by Wang0
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Comment: C: Why ranges of narrowPeak file and that of bed file are not identical
... Sorry! I'm newbie here. Maybe I should edit the original post and append these informations. ...
written 17 days ago by Wang0
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Comment: C: Why ranges of narrowPeak file and that of bed file are not identical
... Thank you,I really appreciate it! Is there any detailed materials or article I can read? I failed to find these information in the official README.md ...
written 17 days ago by Wang0
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Comment: A: Why ranges of narrowPeak file and that of bed file are not identical
... I run macs2 this way macs2 callpeak -t ff.bam -c input.bam -n ff -f BAM -g mm `ff.bam` and `input.bam` was sorted by samtools samtools sort -@ 32 1.bam >ff.bam samtools sort -@ 32 2.bam >input.bam ...
written 17 days ago by Wang0 • updated 17 days ago by RamRS22k
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Comment: C: Why ranges of narrowPeak file and that of bed file are not identical
... ok,I got it!.thank you! ...
written 17 days ago by Wang0
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Why ranges of narrowPeak file and that of bed file are not identical
... Hi everyone! I did peak call using MACS2 to analysis a Chip-seq data and I found the ranges in the narrowPeak file is not same as that in the bed file.what dose this mean?and why?Thanks! more ff_peaks.narrowPeak chr1 3044565 3044674 ff_peak_1 97 . 3.97001 12.89295 ...
macs2 chip-seq sequencing written 17 days ago by Wang0 • updated 17 days ago by ATpoint17k
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Comment: C: If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
... That's interesting! I removed duplications by samtools rmdup while after peak calling using MACS2 I got the same results as that without remove duplications wc -l ko_*.narrowPeak 125573 ko_nodup_peaks.narrowPeak 125573 ko_peaks.narrowPeak So "since MACS2 will ignore them anyway yo ...
written 18 days ago by Wang0 • updated 18 days ago by genomax68k
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Comment: C: Analysis of RNA-seq data of Ion Torrent
... Thank you so much for those useful information! I really appreciate it! ...
written 5 weeks ago by Wang0
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Comment: C: Analysis of RNA-seq data of Ion Torrent
... I'd like do differential expression analysis.Or further pathway clustering,network analysis if possible. ...
written 5 weeks ago by Wang0
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Analysis of RNA-seq data of Ion Torrent
... Hi, everyone. I'm a newbie to sequence data analysis. Yesterday I came across a sequence data created by Ion Torrent form GEO(GSEGSE89972).I plan to analysis the SRA data downloaded from GEO, but I just wonder how can I analysis these data properly. The same as those from Illumina?Are the pipelines ...
rna-seq written 5 weeks ago by Wang0 • updated 5 weeks ago by lshepard340

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