User: star

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star60
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Posts by star

<prev • 61 results • page 1 of 7 • next >
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(Closed) aligning using bowtie2?
... I am doing aligning with bowtie2 and just need reads that aligned exactly 1 time. so I have performed 2 ways: but I am not sure whether the first one is correct or not, while most of literature used the second one? 1= bowtie2 --very-sensitive --score-min C,0,0 --> that number of aligned exactly ...
genome R alignment chip-seq rna-seq written 24 days ago by star60
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Comment: C: shift direction in ATAC/DNase data?
... Thanks for your reply! is it necessary to use `--nomodel` for PE reads, I mean just use `-f BAMPE`. How about when there is SE reads, shall we use `--nomodel --shift -100 --extsize 200`? ...
written 24 days ago by star60
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shift direction in ATAC/DNase data?
... I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS2, but I found that there are some differences in shift size (plus or minus direction). I like to know which one is better for either ATAC-seq or DNase-seq `(e.g. --nomodel --shift -100 --extsize 200 or ...
macs2 chip-seq atac-seq dnase-seq written 25 days ago by star60
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Can be merged biological replicates?
... Can we merge/ combine biological replicates from same sample together in ChIP-seq / ATAC-seq data when we want to do peak calling (or like RNA seq we should process each replicate separately)? because I am seeing in some papers, the data were merged for peak calling and some where else processed sep ...
chip-seq macs2 peak-calling atac-seq rna-seq written 4 weeks ago by star60
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why is there still duplication after extracting aligned read exactly 1 time?
... I have some ChIP seq data that I have done aligning with bowtie2 --very-sensitive --score-min C,0,0 and then extract aligned read exactly 1 time and then remove duplication using Picard tools. I like to know why we have still duplication while I have extracted only aligned read exactly 1 time? T ...
duplicate alignment chip-seq samtools rna-seq written 4 weeks ago by star60 • updated 4 weeks ago by ATpoint7.5k
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Comment: C: merge multiple data with multiple columns?
... Just I did , join data1.bed data2.bed > data.bed ...
written 6 weeks ago by star60
1
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1
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merge multiple data with multiple columns?
... I have multiple data that in all of them the first 3rd columns are the same and I like to merge those data based on these three columns. I can do it with merge command in R but I like to do it in Linux (I used joint command but it does not work well). data1: chr1 724060 724400 SK chr1 7 ...
script linux written 6 weeks ago by star60
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5
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Comment: C: extract only rows eith numbers?
... yes, exactly, I want just main chromosomes. ...
written 6 weeks ago by star60
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7 follow
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Extract only rows with main chromosomes (1-22, X, Y) on first column?
... I have a table like below, it is a bed file of genome coordinate, I would like to keep only rows with numbers. Input: 1 141009669 141009952 9 141016322 141016973 GL000195.1 81719 82468 GL000195.1 142613 142923 GL000220.1 119445 119746 HG115_PATCH 101957832 1 ...
R grep script linux written 6 weeks ago by star60 • updated 23 days ago by benformatics270
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214
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How to filter/edit some BED lines.
... I have two tables and I did intersect using bedtools, but after interacting i just get coordinate as out put and I would like to know how can I add one column to out put using If and else function? data A: chr1 59362359 59364245 chrX 112062100 112062600 chrX 118920850 118927075 data ...
bedtools linux written 12 weeks ago by star60 • updated 4 weeks ago by Biostar ♦♦ 20

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