User: Lucy

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Lucy0
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Posts by Lucy

<prev • 9 results • page 1 of 1 • next >
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FRIP score ATAC-seq
... Hi, I am trying to calculate the fraction of reads in peaks (FRIP score) for my ATAC-seq samples. What I have so far is written below, however I think it is wrong somehow as I am getting a very low score (when I calculate the FRIP using DiffBind, it comes out much better/more like the expected val ...
frip atac-seq written 11 days ago by Lucy0 • updated 6 days ago by chaton0
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Comment: C: Determine peak summits after IDR analysis
... Thank you. Please could you explain the first part in more detail. I would take column 10 from my .narrowPeaks file, which is the relative summit position and place this into the fifth column of which file? ...
written 12 days ago by Lucy0
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Comment: C: Determine peak summits after IDR analysis
... macs2 was used for the initial peak calling ...
written 13 days ago by Lucy0
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Determine peak summits after IDR analysis
... Hi, I have performed ATAC-seq on three different cell subsets and have generated an optimal peak list for each using IDR analysis. I then ran bedtools merge to generate a global peak list for all of the subsets combined. However, by merging the peaks, I lose the summit information i.e. some peaks ...
peak summits macs2 idr written 13 days ago by Lucy0 • updated 12 days ago by Alex Reynolds25k
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Comment: C: When using MACS2 with -f BAM, it is possible to have a shift other than 0?
... Yes this is ATAC-seq data. ...
written 13 days ago by Lucy0
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Comment: C: ATAC-seq peak calling with MACS
... Is --nomodel not required if you are using -f BAMPE? ...
written 26 days ago by Lucy0
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Comment: C: shift direction in ATAC/DNase data?
... I am confused as to why so many papers use --shift -100 --extsize 200 for ATAC-seq data if this is not recommended for paired-end data? What is the reason for doing the shift and extsize? ...
written 27 days ago by Lucy0
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When using MACS2 with -f BAM, it is possible to have a shift other than 0?
... Hi, In the manual for MACS2, there is the following statement in the information about the --shift option: "Note, you can't set values other than 0 if format is BAMPE or BEDPE for paired-end data. Default is 0" Is this also the case if the format is set as BAM or can I have different shift sizes w ...
macs macs2 written 28 days ago by Lucy0 • updated 10 hours ago by Biostar ♦♦ 20
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Should --very-sensitive be combined with -no-1mm-upfront?
... Hi, I am planning to use the --very-sensitive option for aligning my ATAC-seq reads. However, after reading the manual section below, I am unclear as to whether this option should be combined with --no-1mm-upfront or not? > "By default, Bowtie 2 will attempt to find either an exact or a > 1- ...
bowtie2 bowtie written 28 days ago by Lucy0 • updated 28 days ago by Devon Ryan84k

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