User: fusion.slope

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fusion.slope150
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Posts by fusion.slope

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Colors UCSC genome browser
... thanks Emily_Ensembl ...
written 7 days 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 7 days ago by fusion.slope150 • updated 7 days ago by Emily_Ensembl15k
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List of Genes According to Ontologies
... Hello, I was wondering if there is a website in which I can retrieve the list of genes for each ontology. For example for the biological process "Regulation of Gene Expression," I would like to have all the list that belong to this ontology etc.. Thanks in advance ...
genome gene written 10 days ago by fusion.slope150 • updated 10 days ago by Pierre Lindenbaum108k
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Comment: C: Y axis PlotHeatMap Deeptools
... Thanks Devon, the fact is that am seeing that in my Plot the numbers do not correspond.. https://ibb.co/huvoJJ Can you see it? Thanks in advance for any comment ...
written 19 days ago by fusion.slope150
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Y axis PlotHeatMap Deeptools
... Hello, am wondering what values are represented in the Y axis of plotHeatMap in Deeptools.If we consider the first picture here: http://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html What are the values in the Yaxis on top left (on the box) and what are the values on the righ ...
deeptools written 19 days ago by fusion.slope150 • updated 19 days ago by Devon Ryan80k
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Comment: C: How Do you find constitutive exons in Ensembl or UCSC
... I tried to run this for hg19 but it does not work. Is it correct to use: "http://hgdownload.cse.ucsc.edu/goldenPath/**hg19**/database/**wgEncodeGencodeCompV19.txt.gz** instead of "http://hgdownload.cse.ucsc.edu/goldenPath/**hg38**/database/**wgEncodeGencodeCompV27.txt.gz** and "http://hgdo ...
written 3 months ago by fusion.slope150
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... in two samples we had ~ 60% of the reads un mapped in other 2 we have 35% (each sample had ~ 450 mil reads in paired end so ~900 mil). Why hardware and software issues? I have done all the checksums and the files were transfered in the correct way (output of checksums was ok). Could you please tell ...
written 9 months ago by fusion.slope150
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... I took the un mapped reads and blasted them without any success. I have mapped the un mapped reads to the genome of lambda virus and micoplasma with not success (in both cases very few reads mapped ). I am speculating that the mappability is related with the tiles because according to the quality of ...
written 9 months ago by fusion.slope150
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... Hi br.m, sorry for the late reply. Basically i did a bash script removing the tiles in the red color. Unfortunately the mappability of my samples removing those tiles remains the same.. As I am understanding from your pictures, you have even worst "per tile sequencing quality". I am sorry but I do ...
written 9 months ago by fusion.slope150
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Comment: C: Selecting Random Pairs From Fastq?
... he told you that is the random seed. Something that is used in any initial simulation step. In R is set.seed for example before perform simulation.. ...
written 9 months ago by fusion.slope150

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