User: juanpjlozano

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Posts by juanpjlozano

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Answer: A: 40-50% reds mapping to genome in a ChIP Seq experiment
... I got a similar problem and found human contamination (I study Drosophila). I would recommend to use fastq_screen, it will do a very basic alignment to different genomes. If that doesn't account for the ~50% unaligned reads, then blast some of the unaligned reads. ...
written 4 weeks ago by juanpjlozano0
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Comment: C: Dealing with spike-in reads that overlap between two genomes
... no, the plant chromatin is used for signal normalization, it is supposed to account for IP technical variation between samples. I pretty much add same amount of plant chromatin to each one of my "real" Drosophila samples. Currently I am doing the genome combination and filtering, we'll see what happ ...
written 9 weeks ago by juanpjlozano0
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Dealing with spike-in reads that overlap between two genomes
... I recently did a histone ChIPseq experiment. I study Drosophila and used Arabidopsis chromatin as spike-in. After trimming the raw reads and aligning with bwa (reads were 150 PE), for some of my input samples, I got that 60% of my reads aligned to Drosophila and 50% aligned to Arabidopsis. Do you gu ...
drosophila spike-in arabidopsis chip-seq written 9 weeks ago by juanpjlozano0 • updated 9 weeks ago by colin.kern510

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