User: izzy.yichao.cai

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Posts by izzy.yichao.cai

<prev • 49 results • page 1 of 5 • next >
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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 6 months ago by izzy.yichao.cai110
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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 6 months ago by izzy.yichao.cai110
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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 6 months ago by izzy.yichao.cai110
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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 6 months ago by izzy.yichao.cai110 • updated 6 months ago by Malcolm.Cook790
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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 7 months ago by izzy.yichao.cai110
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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 7 months ago by izzy.yichao.cai110
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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 13 months ago by izzy.yichao.cai110
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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 13 months ago by izzy.yichao.cai110
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Comment: C: How to properly combine two bam files of a paired-end data
... The point is that the paired-end reads that I got might cross a very very long distance along the chromosome, and even the two tag of the paired-end reads are on different chromosomes. If I subject the two fastq file and run bowtie2 in paired-edn mode, some reads might not be mapped to the genome ...
written 13 months ago by izzy.yichao.cai110
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Comment: C: How to properly combine two bam files of a paired-end data
... Hi I tried fixmate but it doesn't seem to working. Here is what i did: 1) Sort the two bam files by name. 2) use samtools merge to merge two bam files. 3) sorted the merged bam files by name. 4) samtools fixmate But still, there are no properly-paired reads. (0 + 0 paired in sequencing; 0 + 0 read ...
written 13 months ago by izzy.yichao.cai110

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Popular Question 27 days ago, created a question with more than 1,000 views. For using bedtools to find the intersect of bedpe and bed
Popular Question 4 months ago, created a question with more than 1,000 views. For SRA toolkit not installed
Popular Question 5 months ago, created a question with more than 1,000 views. For SRA toolkit not installed
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Popular Question 7 months ago, created a question with more than 1,000 views. For Difference between blastp and phi-blast
Popular Question 11 months ago, created a question with more than 1,000 views. For How to convert UCSC ID to gene symbol
Popular Question 11 months ago, created a question with more than 1,000 views. For ChIP-seq peak calling & visualized in IGV
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