User: marongiu.luigi

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Posts by marongiu.luigi

<prev • 155 results • page 1 of 16 • next >
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Comment: C: Is there a perfect WGS dataset?
... I even got a dataset reported from a manual (I won't say which one) and the base quality figure is as good as in the book; what they did not show was the associated summary: ![enter image description here][1] also, this was an exome analysis, not WGS... [1]: http://u.cubeupload.com/gigux/276Scre ...
written 21 hours ago by marongiu.luigi190
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Comment: C: Is there a perfect WGS dataset?
... thank you, that would be the perfect answer but the access is restricted: from the website is reported > Extramural Investigators must be permanent employees of their > institution at a level equivalent to a tenure-track professor or > senior scientist with responsibilities that most like ...
written 21 hours ago by marongiu.luigi190
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Comment: C: Is there a perfect WGS dataset?
... I just need a didactical dataset that shows how fastqc works, but all the datasets I have available show some defect of some sort. I still haven't found one that does not have any flag raised. I need to produce a figure like that one sees in the manual, but without a good dataset, I cannot. I could ...
written 22 hours ago by marongiu.luigi190
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Is there a perfect WGS dataset?
... Hello I was wondering whether there is an Illumina WGS dataset (fatsq files) that is quality control flaw-less, something that does not have yellow of red flags in any of the FASTQC fields, no tile errors or kmers, for instance but shows the typical decreased of quality values at the extremities. ...
next-gen sequence written 22 hours ago by marongiu.luigi190 • updated 21 hours ago by Pierre Lindenbaum108k
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Sequence Length Distribution after trimmomatic
... Hello, I have trimmed my sequences with TRIMMOMATIC using the following command: trimmomatic.sh PE -phred33 -threads 8 LEADING:13 TRAILING:13 SLIDINGWINDOW:7:30 MINLEN:30 I think the trimming has been a good thing to do because the quality control (performed with FASTQC) shows slight ...
next-gen sequence written 4 days ago by marongiu.luigi190
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Comment: C: when to merge lane replicates?
... perfect, thank you! now it is clear ...
written 10 days ago by marongiu.luigi190
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when to merge lane replicates?
... Dear all, I have a set of samples each having multiple lane's replicates. When shall I merge the different replicate? BEFORE (that is, merge the fastq files) or AFTER (that is, merge the BAM files) the alignment? Does the step of merging varies if the study is WGS or RNAseq? I haven't found a str ...
alignment next-gen written 11 days ago by marongiu.luigi190 • updated 10 days ago by genomax49k
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Comment: C: How to select an aligner?
... Well, who said I stopped using BWA? It is just that if there is a faster and more multipurpose aligner, the future analysis might be faster... The main problem, as it has been pointed out, is the interlink with the downstream applications. So probably Friederike is right: there is the need for some ...
written 16 days ago by marongiu.luigi190
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Comment: C: How to select an aligner?
... Because, from experience, I find HISAT faster than BWA... ...
written 17 days ago by marongiu.luigi190
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Comment: C: How to select an aligner?
... that's the point: it is possible to move out from BWA? I have the impression that BWA is widely used for historical reasons more than a fundamental link between BWA and GATK... ...
written 17 days ago by marongiu.luigi190

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