User: int11ap1

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int11ap1380
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Posts by int11ap1

<prev • 120 results • page 1 of 12 • next >
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Reproducibility Exon imbalance
... Dear all, I am trying to reproduce the exon imbalance analysis from this paper (specifically, Figure 1C): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184927/ Authors normalize raw coverages as described below (from supplementary materials): ![enter image description here][1] [1]: https://i.ib ...
exon imbalance written 9 months ago by int11ap1380
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Hi-C, compartments, issue with some chromosomes
... Hi, I calculated the first PC1 (first eigenvector) of a Hi-C matrix. Some chromosomes look good, some others like the following one not: ![enter image description here][1] [1]: https://image.ibb.co/hfPpab/chr22.png In green, the first eigenvector. At the second layer, in blue, compartments B. ...
hi-c compartments written 2.1 years ago by int11ap1380
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Protein sequences to where they bind to the genome
... I have a multifasta with multiple sequence proteins. My aim is to locate the sites in the genome they bind to. Is that possible? ...
protein multialignment written 2.2 years ago by int11ap1380
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Comment: C: Human in NCBI Genomes
... I said GFF in the post. ...
written 2.3 years ago by int11ap1380
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Human in NCBI Genomes
... I want to download the human annotation from NCBI Genomes. Searching the term *human* in [https://www.ncbi.nlm.nih.gov/genome/][1] I redirects me into [https://www.ncbi.nlm.nih.gov/genome/?term=human][2] So, when I click to GFF in order to download the annotation, the downloaded file is way too ...
genome ncbi human written 2.3 years ago by int11ap1380 • updated 2.3 years ago by vmicrobio240
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Answer: A: Amd Or Intel Based Workstation For Bioinformatics?
... I've just found this workstation: [http://www.ebay.es/itm/-/322567393191?][1] What's your opinion about it? [1]: http://www.ebay.es/itm/-/322567393191? ...
written 2.4 years ago by int11ap1380
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Hi-C contact probability
... I was wondering, if I have a Hi-C matrices and the average ICE-normalized interaction vs. genomic distance, how can I create a plot like the following one? ![enter image description here][1] I created something similar: ![enter image description here][2] but it's not contact probability. I want ...
hi-c written 2.6 years ago by int11ap1380
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FASTQ header format, direction or pair number
... I have the following headers: Pair 1: @NS500352:99:HMFTGBGXY:1:11101:14196:1038 **1:**N:0:ATCACG Pair 2: @NS500352:99:HMFTGBGXY:1:11101:14196:1038 **3:**N:0:ATCACG Why pair 2 has a value of **3** in the read number field? Shouldn't it be 2? ...
fastq written 2.8 years ago by int11ap1380
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Comment: C: MAKER annotation gives weird results
... I have edited my post with the content of maker_opts.ctl. ...
written 3.1 years ago by int11ap1380
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MAKER annotation gives weird results
... I am performing a gene annotation on an assembly and, for a specific loci, I have the following support: ``` Pp05 blastn expressed_sequence_match 11506941 11508983 2043 + . ID=Pp05:hit:646548:3.2.0.2;Name=asmbl_43336 Pp05 est2genome expressed_sequence_match 11506941 11508983 10215 + . ID=Pp05:hit:6 ...
gene annotation maker written 3.1 years ago by int11ap1380

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Commentator 6 months ago, created a comment with at least 3 up-votes. For C: GATK_HaplotypeCaller: .
Popular Question 7 months ago, created a question with more than 1,000 views. For Hi-C data and structural variations
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For GO Enrichment Analysis representation

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