User: fusion.slope

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fusion.slope130
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Posts by fusion.slope

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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 weeks ago by fusion.slope130
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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 weeks ago by fusion.slope130
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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 weeks ago by fusion.slope130
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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 12 weeks ago by fusion.slope130
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Comment: C: Sequence Bias Bismark Output Interpretation
... Here the explanation about how to solve the problem: https://sequencing.qcfail.com/articles/library-end-repair-reaction-introduces-methylation-biases-in-paired-end-pe-bisulfite-seq-applications/ ...
written 12 weeks ago by fusion.slope130
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Answer: A: Sequence Bias Bismark Output Interpretation
... I found a good answer here: https://sequencing.qcfail.com/articles/library-end-repair-reaction-introduces-methylation-biases-in-paired-end-pe-bisulfite-seq-applications/ ...
written 4 months ago by fusion.slope130
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Sequence Bias Bismark Output Interpretation
... Hello Community, I have performed with Bismark the M-Bias Plot and my reads looks as follow. ![CpG Bias][1] [1]: https://i.imgur.com/Ce6tsgn.png as far as I am understanding the end of read 1 is showing a decrease in the CpG Methylation at the 3'end as well as the CHH total and CHG in the to ...
sequence bias m-bias plot methylation cpg written 5 months ago by fusion.slope130
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... yes thanks lets wait for the output also... ...
written 5 months ago by fusion.slope130
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... o wait, i did the quality with the same file :((, let me modify the previous report and lets wait for the output of the quality check with the output of "filterbytile.sh" script.. i think in less than 1 hours i have the output in the meantime here is the output of the script: java -ea -Xmx91147 ...
written 5 months ago by fusion.slope130 • updated 5 months ago by genomax37k
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Comment: C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
... Hi Brian, I have tried 'filterbytile' from bbmap and am doing now the quality check with fastqc. Meanwhile i made a unix command to remove all the reads that are in those tiles signed as red in the heat map. Before removing: pic upload edit After Removing: get url for picture As you can see there ...
written 5 months ago by fusion.slope130

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