User: izzy.yichao.cai

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Posts by izzy.yichao.cai

<prev • 51 results • page 1 of 6 • next >
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Comment: C: How to align reads to only one strand on a haploid reference genome?
... Jeez. I think I mistakenly think that haploid genome has only one strand of DNA. :p I ask a silly question. Though it is haploid, the DNAs are still double-stranded (Just that it has only 23 chromosomes). Thanks for pointing out! ...
written 10 months ago by izzy.yichao.cai140
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How to align reads to only one strand on a haploid reference genome?
... Hi folks, I have a set of ChIP-seq data from a haploid cell line. How do I map the reads to only one strand of my haploid genome since the reads can only come from one strand? Thank you so much! ...
genome alignment chip-seq sequencing written 10 months ago by izzy.yichao.cai140
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Interaction calling using contact matrix
... Hi all, Does anyone get a clue on how to call chromatin interactions from a HiC contact matrix? I found this useful software collection: https://www.4dnucleome.org/software.html . However, the most majority of them involved in mapping reads and generating/comparing contact matrix. There are some ...
next-gen sequencing written 17 months ago by izzy.yichao.cai140
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Comment: C: Merge two bigwig(+/- strand) files from RNA-seq
... Emmm. I am not that familiar with python. By a quick browse at the pyBigWig package, I need to first convert all the signal value in the negative strand to positive value, and then generate a new bigwig file with header and new value. Then I can use other tools like BigWigMerge from UCSC to merge my ...
written 17 months ago by izzy.yichao.cai140
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Comment: C: Merge two bigwig(+/- strand) files from RNA-seq
... Looks promising, but the installation is a pain. I am still trying to get it installed. ...
written 17 months ago by izzy.yichao.cai140
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Merge two bigwig(+/- strand) files from RNA-seq
... Hi all, I am working on expression data from EpigeneticRoadmap and wanted to generate an expression track.([Link here][1]) Since the cell line expression data only has bigwig file in two separate files. One from **positive strand**; the other from **negative** strand and has **negative values**. U ...
next-gen rna-seq sequencing written 17 months ago by izzy.yichao.cai140 • updated 17 months ago by Malcolm.Cook870
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Comment: C: Weird Kmer at 5' of read 1 in paired-end RNA-seq
... LOL. Noticed that already. Thanks for the correction! ...
written 19 months ago by izzy.yichao.cai140
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Weird Kmer at 5' of read 1 in paired-end RNA-seq
... Hi all, I've come across a weird issue with my RNA-seq data. Some details about the data: There 4 libraries of RNA, all total RNA-seq in wild-type and mutant cell with 2 replicate. Total 2 wild-type(Lane1, Lan2) + 2 mutant(Lane3, Lane4). 1. Platform: Ilumina Truseq 2. Prep kit: TruSeq LT Kits a ...
next-gen rna-seq sequencing written 19 months ago by izzy.yichao.cai140
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Comment: C: How to properly combine two bam files of a paired-end data
... Yes, they are of the same name. Okay, I got what you mean. It seems that I am too particular on "properly paired end". :p But then I found another problem, which is that the sorted bam file has a different order of lines. This result in the empty result of bedpe file when I subject the merged bam ...
written 2.0 years ago by izzy.yichao.cai140
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Comment: C: How to properly combine two bam files of a paired-end data
... Hi, can BWA map long distance/discordant read pairs? The [relative new paper][1] on ChIA-PET data pipeline also aligns two ends of reads independently to the genome even using BWA. [1]: http://nar.oxfordjournals.org/content/early/2016/09/12/nar.gkw809.full ...
written 2.0 years ago by izzy.yichao.cai140

Latest awards to izzy.yichao.cai

Popular Question 10 months ago, created a question with more than 1,000 views. For Download all chip-seq data of a cell type in ENCODE
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Popular Question 12 months ago, created a question with more than 1,000 views. For using bedtools to find the intersect of bedpe and bed
Popular Question 16 months ago, created a question with more than 1,000 views. For SRA toolkit not installed
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Student 2.5 years ago, asked a question with at least 3 up-votes. For using bedtools to find the intersect of bedpe and bed

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