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Search: Posts Made By: cloverliang
Forum: Bioinformatics 08-28-2015, 06:28 AM
Replies: 22
Views: 20,933
Posted By cloverliang
Thank you baritone!! I'm looking for TF binding...

Thank you baritone!! I'm looking for TF binding footprints, which presumably have less transposase cuts compared to its flanking region. So I wanted to trim reads to the 1bp cutting position. The...
Forum: Bioinformatics 08-27-2015, 07:03 AM
Replies: 22
Views: 20,933
Posted By cloverliang
Hi Dariober, I'm also analyzing ATAC-seq...

Hi Dariober,

I'm also analyzing ATAC-seq data. I did in a similar way to your procedure:

1. Map to hg19 with bowtie2 (-X 2000).
2. Remove reads with MAPQ < 10 and sort bam file using...
Forum: Bioinformatics 08-26-2015, 08:00 AM
Replies: 0
Views: 2,025
Posted By cloverliang
ATAC-seq cutting frequency analysis

Hi everyone!

I'm analyzing ATAC-seq data. But I got problems in observing nice peaks as shown in Fig. 1c. in Buenrostro 2013 nature method paper.

I have the following steps:
1. Map to hg19...
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