User: fusion.slope

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fusion.slope150
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Posts by fusion.slope

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Comment: C: gene_Id in ENCODE gene expression table
... oh thanks a lot, I have scrolled a bit the file but did not go down enough to see the ENSEMBL gene annotation! much appreciated genomax! ...
written 19 days ago by fusion.slope150
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Comment: C: gene_Id in ENCODE gene expression table
... thanks a lot, i think alex already answered my question :) but to confirm i should check rsem output to see which gene_id reference they use.. ...
written 19 days ago by fusion.slope150
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Comment: C: gene_Id in ENCODE gene expression table
... For example the tsv file here: https://www.encodeproject.org/experiments/ENCSR000CPH/ click in file details ...
written 19 days ago by fusion.slope150
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Comment: C: gene_Id in ENCODE gene expression table
... I have a list of genes. I will take some genes that I know the name in the Gene Id and check in this website you suggested if they match. Then i will use http://biodb.jp/ to convert. Thanks for the info. ...
written 19 days ago by fusion.slope150
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gene_Id in ENCODE gene expression table
... Hello, I would like to use the expression value of some genes in the ENCODE project. I have a table with me but I can notice that the name of the genes is just a number. Does anyone know which format is it? Here example: https://ibb.co/gcefj9 Does anyone know the name of this format s ...
gene encode conversion written 19 days ago by fusion.slope150
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Comment: C: Sequence Bias Bismark Output Interpretation
... Yes I got your point, and sorry if i did not get your full concern at the first time. What i can tell you from my experience is that in the read 2 for CHG or CHH there is always that kind of drop, why i do not know. Since I was mostly interested in the CpG (where the trend of the methylation values ...
written 3 months ago by fusion.slope150
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Comment: C: Sequence Bias Bismark Output Interpretation
... if you read the link I sent you is exaplained (even though is not a clear explanation): "The methylation state of the first couple of bases or Read 2 drops from the average ~70% down to ~3%, and this steep drop can certainly be explained by the filled-in unmethylated cytosines. Since there is no re ...
written 3 months ago by fusion.slope150
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Comment: C: Sequence Bias Bismark Output Interpretation
... here the explanation about R2: https://sequencing.qcfail.com/articles/library-end-repair-reaction-introduces-methylation-biases-in-paired-end-pe-bisulfite-seq-applications/ you can try to have a better performance using this command in Bismark: bismark_methylation_extractor --ignore_r2 2 --gzip s ...
written 3 months ago by fusion.slope150
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Comment: C: Colors UCSC genome browser
... thanks Emily_Ensembl ...
written 4 months ago by fusion.slope150
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Colors UCSC genome browser
... Hello, does anyone know the code for each color of UCSC genome browser? Is there a list or something? For example this one "color=250,0,0" gives me the color RED and this one "color=0,0,250" is blue. Is there a list in which i can select the serial number for other colors? Thanks in advance ...
custom track colours ucsc written 4 months ago by fusion.slope150 • updated 4 months ago by Emily_Ensembl16k

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