User: crisime

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crisime180
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Posts by crisime

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Number of sequence copies per cluster on Illumina?
... Hi Brian, I don't know the details on a flowcell, but never thought of the process as just "growing one step 2-dimensinal" like "occupy the closest field on a chess-board like the pawn". I always assumed sequences to be long enough to jump a few binding sites/fields further like the knight. And the ...
written 12 weeks ago by crisime180
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Number of sequence copies per cluster on Illumina?
... Hi, when proofreading for a colleague I just stumbled upon an unreferenced claim that we have thousands to millions of sequence copies in each cluster using Illumina technology. Wikipedias [Illumina dye sequencing][1] can't decide between "about a thousand" and "hundreds" referencing just one [art ...
next-gen sequencing written 12 weeks ago by crisime180
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Comment: C: What are the available methods to detect cross-sample contamination of NGS data?
... Still viable for human cross-sample contamination detection, if your samples have different target regions. You just have to define your target regions as the genomes for FastQ Screen. ...
written 4 months ago by crisime180
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Answer: A: What are the available methods to QC NGS data for sample contamination
... If you work with different species or different target regions per sample, have a look at [FastQ Screen][1] [1]: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ ...
written 4 months ago by crisime180
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Comment: C: Ensembl ID differences between assemblies?
... The IDs may stay the same but the information (your entity) they are pointing to can change quite a lot! Same ENST may point to a - different gene/ENSG (see my answer below) - different sequence (https://www.biostars.org/p/251935/, https://www.biostars.org/p/154539/ ) - ... in different buil ...
written 5 months ago by crisime180
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Answer: A: Ensembl ID differences between assemblies?
... Hi jiab, to give you an idea of the differences here is a little bash script, which gives you a list of ENSTs mapping to different ENSGs in grch37 and grch38: #!/bin/bash #download of all ENST mapped to ENSG from Ensembls grch37 biomart wget -O mapping_37.txt 'http://grch37.ensembl.org ...
written 5 months ago by crisime180
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Answer: A: Two Ensembl Transcript Ids seem swapped with respect to AA sequence in different
... Hi mtscales, I had a similar problem with ENST instability even in the same genome build some time ago. I summarised the answer from the Ensembl helpdesk here in my own question: https://www.biostars.org/p/154539/ I first thought here it is the same. It is not what you expect for a stable ID. But ...
written 6 months ago by crisime180
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Answer: A: How to cite Ensembl
... They have answered it in their FAQs: http://www.ensembl.org/Help/Faq?id=392 You can find the current version/release on the bottom left of each Ensembl Page. ...
written 13 months ago by crisime180
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Comment: C: I am really pissed off by the bioinformatics software world. Do/can we have a be
... As a short intro to think about maybe this: [Creating great documentation for bioinformatics software][1] [1]: https://tspace.library.utoronto.ca/bitstream/1807/73111/1/great-documentation-bioinformatics.pdf ...
written 14 months ago by crisime180
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Answer: A: What Is Rationale Behind UCSC/Ensembl Canonical Transcripts?
... answering UPDATE/ENSEMBL: For human it is defined in the ensembl glossary: http://www.ensembl.org/Help/Glossary?id=346   "Canonical transcript: For human, the canonical transcript for a gene is set according to the following hierarchy: 1. Longest CCDS translation with no stop codons. 2. If no ...
written 23 months ago by crisime180

Latest awards to crisime

Popular Question 7 days ago, created a question with more than 1,000 views. For Stability of Ensembl and refseq stable IDs
Scholar 5 months ago, created an answer that has been accepted. For A: Stability of Ensembl and refseq stable IDs
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Two Ensembl Transcript Ids seem swapped with respect to AA sequence in different
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Two Ensembl Transcript Ids seem swapped with respect to AA sequence in different
Scholar 15 months ago, created an answer that has been accepted. For A: Stability of Ensembl and refseq stable IDs
Student 2.2 years ago, asked a question with at least 3 up-votes. For Stability of Ensembl and refseq stable IDs
Supporter 2.2 years ago, voted at least 25 times.

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