User: Gene

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Gene 20
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Posts by Gene

<prev • 11 results • page 1 of 2 • next >
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How to exclude reads with five or more variations from the reference
... I am working on SNP analysis. Sequencing was performed by Molecular Inversion Probe (MIP)-based re-sequencing. I have BAM files right now, and I am trying to **eliminate reads with more than five variations from the reference per read**, with the exception of multi-basepair insertions and deletions. ...
sequencing written 5 months ago by Gene 20
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Comment: C: Plotting - taking size and mean in consideration
... Thank you for idea. I thought also about boxplots with width, but I have a lot of genes, and ideally it would be to represent all exons of one gene together. Overall mean should be influenced by size. Something like weightened mean - mean of 16.4791415 should contrubute 46 % to overall mean, becau ...
written 7 months ago by Gene 20
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Plotting - taking size and mean in consideration
... Dear all, I have one doubt. I do not know which plot to choose which will represent my data well. exon mean exon size exon 1a 222.6731781 145 exon 1b 268.3251009 135 exon 1c 142.7838168 90 exon 1d 289.7393662 ...
plot written 7 months ago by Gene 20 • updated 7 months ago by lessismore890
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Comment: C: How to implement Hadoop as non map/reduce ?
... Yes, just for testing, as a second task in our Project. ...
written 7 months ago by Gene 20
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How to implement Hadoop as non map/reduce ?
... We are bachelor students working on programming project. We need to use Hadoop and Java. Our application loads a FASTQ document, counts IDs, read length, count all bases, perfoms k-mer analysis. We implemented it as a Map/Reduce Approach. Now, my question is how to use Hadoop in a non map/reduce m ...
hadoop java next-gen fastq non map/reduce written 7 months ago by Gene 20
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Comment: C: NGS data processing with Hadoop
... We have done it already. All plots from FASTQC were generated. Now we are thinking of how to integrate it with Hadoop -.- Thank you for the suggestion. ...
written 8 months ago by Gene 20
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Comment: C: Aggregating coverage values exon wise
... Thank you for your response. I am not that familiar with R, but will try to code it then in Python. ...
written 8 months ago by Gene 20
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Aggregating coverage values exon wise
... I have exon ranges, for example: > > Chr_exon start - exon end > > 1_3774167-1_3774281 > > 1_3775281-1_3775430 > > 1_3782281-1_3782564 > > 1_3784537-1_3784617 > > 1_3786168-1_3786339 > > 1_3789035-1_3789136 > > 1_3800070-1_3800305 And also, I ...
ngs exon coverage aggregation written 8 months ago by Gene 20 • updated 8 months ago by Kevin Blighe63k
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Plotting - Coverage Analysyis
... I have a big file containing information about coverage depth. File is in format chr_position samp1-depth value samp2-depth-value samp*-depth value ... ( a lot of samples: 100 +) I want to generate a plot which will be the most appropriate representation of my data. This i ...
R sequencing python coverage plot written 9 months ago by Gene 20 • updated 9 months ago by zx87549.4k
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Comment: C: Combining files based on chromosome and position next to each other - column vi
... Thank you a lot. It was really helpful and it is working. ...
written 9 months ago by Gene 20

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