User: cjgunase

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cjgunase20
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14 hours ago
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2 years, 6 months ago
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c*******@mtu.edu

Posts by cjgunase

<prev • 19 results • page 1 of 2 • next >
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LD Plot like diagram to cluster genomic regions (bins)
... I want to cluster the genomic bins based on pairwise correlation > 0.75 into by sequentially traversing the table. (sample is shown in the image). If correlated the bins are averaged and the next bin is considered. soon the correlation is calculated sequentially until the criteria (0.75) fails. a ...
ld plot sequential correlation written 6 months ago by cjgunase20
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USCS visualization track for genomic bins
... Hi, I am looking for a way to display the following information in a UCSC browser or JBrowse . Can anyone please give me an idea or method to covert the data are shown here. Or how to convert to WIG format so I can import to the browser. Bin.Location chr Perc.Methy 49393000 19 0.95564 ...
genome browser visualization ucsc written 6 months ago by cjgunase20 • updated 4 months ago by max10
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Comment: C: samtools: writing to standard output failed: Broken pipe
... the same thing happened to me as well. This is the end of fhe PBS output file. but I got the coverage file. Finished generating genome-wide cytosine report samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 gzip: stdout: Broken pipe ...
written 6 months ago by cjgunase20
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SNP calling for whole genome bisulfite sequencing data as a quality control step
... Hi, we recently received WGBS data from 3 tissues in 10 individuals (30 samples). As a quality control measure, I want to check if any samples were got switched during tissue transfer. So I am planning to do SNP concordance to compare all 30 libraries. This should show high concordance within each i ...
bisulfite-sequencing next-gen sequence written 7 months ago by cjgunase20
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Comment: C: Very low Bisulfite seq mapping efficiency (~0%) for paired end.
... Thankx Devon, I tried BBMap and this script worked even better. now its mapping in paired-end with ~85% https://github.com/enormandeau/Scripts/blob/master/fastqCombinePairedEnd.py Thank you for your effort to help solve this issue. ...
written 8 months ago by cjgunase20
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Comment: C: Very low Bisulfite seq mapping efficiency (~0%) for paired end.
... I did a comparison as you said. Thank you for the idea. I am going to reorder the fastq files. Not aligning sample(1F52S) [gunasekara@sphere fq0050]$ head -1 split.10m.GTEX-1F52S-3026-SM-D5A5F_1.fq @E00591:56:H2LTKCCXY:3:1102:31527:12683 1:N:0 [gunasekara@sphere fq0050]$ head -1 split.10m.GTEX-1F ...
written 8 months ago by cjgunase20
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Comment: C: Very low Bisulfite seq mapping efficiency (~0%) for paired end.
... Thanks Devon, Can you kindly point out how did you find this so I can narrow down where the problem originated? Is there anything to correct this? Thank you ...
written 8 months ago by cjgunase20
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is it possible to do alignment using only the reverse strand as single end ?
... Hello, I tried to do alignment using only the **reverse** strand FASTQ file and the mapping efficiency was very low(0.7%). When using **both** strands 85% (as paired-end) and using **forward** strand again 87% (as single -end). What is the reason for this? ...
dna-seq alignment bismark written 8 months ago by cjgunase20
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Comment: C: Very low Bisulfite seq mapping efficiency (~0%) for paired end.
... yes. FastQC looks perfect on both files. found possible reasons in http://seqanswers.com/forums/showthread.php?t=40496 we believe it is over clustering which can happen in read2. Not sure how to prepare a report so we can request re-sequencing. If you can suggest some tools and packages to do m ...
written 8 months ago by cjgunase20
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Very low Bisulfite seq mapping efficiency (~0%) for paired end.
... Hello, I have **bisulfite** converted fastq files (WGBS) from paired-end reads. when I used bismark using the default setting for paired-end data mapping efficiency is almost zero. Then I tried using read1 and the mapping efficiency is 85%. I have put my mapping report in this link. If anyone can ...
mapping-efficiency bisulfite-seq bismark written 8 months ago by cjgunase20

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