User: Learner

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Learner 130
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Posts by Learner

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Comment: C: how should one treat samples in sequencing
... @genomax Can you tell me what should I do in both cases? do you have any idea how to download those databases? is there any differences between all these annotation tools? ...
written 2 days ago by Learner 130
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how should one treat samples in sequencing
... I have 2 control and 2 tumor samples which I have their exome sequencing data. I want to know if you should combine them after alignment during annotation or after annotation or when would be the best time to combine them ? Or should I treat them separately ? My other question is which database is ...
genomics written 2 days ago by Learner 130
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Comment: C: why GATK makes things more complicated ?
... @Istvan Albert I appreciate your time , thanks. I personally think these tools came to make life easier not more complicated, what is the point of spending hours and hours and still thinking that you are doing something wrong :-) ? I just cannot believe the amount of NIH grant wasted on such stuff ...
written 5 days ago by Learner 130
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Comment: C: why GATK makes things more complicated ?
... @finswimmer I liked your answer already but look at my own steps , way much better :-) now I need to put together stuff so that people will understand each step , if you could help , I appreciate it highly ...
written 5 days ago by Learner 130
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Comment: C: why GATK makes things more complicated ?
... @Pierre Lindenbaum I showed the error here. https://www.biostars.org/p/363063/#363103 now I try to understand how they run their wld scripts , unfortunately not a good workflow whatsoever , no example no description , look at their code !!!! so messy ...
written 5 days ago by Learner 130
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Comment: C: why GATK makes things more complicated ?
... @Pierre Lindenbaum thanks for your reply. I liked it , I have gone to that link 100 times, there is no tap nothing that allow me to write a request, comment or whatever , in the bottom of their page, I asked for confirmations at least 100 times, I don't get any email. I registered with 2 email addre ...
written 5 days ago by Learner 130
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Forum: why GATK makes things more complicated ?
... I have been quite busy for sometimes now using this package. No offend but I found it bloody useless at least from being straightforward if one wants to use it. 1- how one can ask for a help ? ( just google how to ask a question, you go to a page where there is nothing allowing you to ask any ques ...
forum genomics written 6 days ago by Learner 130 • updated 5 days ago by WouterDeCoster36k
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Comment: C: how to go from aligning forward when analyzing whole exome sequencing
... @manuel.belmadani I am trying to use their pipeline but GATK changed, now I cannot use any `RealignerTargetCreator` do you have any suggestion or steps that I should take ? ...
written 6 days ago by Learner 130
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Comment: C: how to perform the RealignerTargetCreator when there is not this algorithm anymo
... @finswimmer but what about the error I get? why I get those errors when I don't use the Indel Realignment ? ...
written 6 days ago by Learner 130
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how to perform the RealignerTargetCreator when there is not this algorithm anymore
... I am trying to use the GATK to realign bam file Normally I could this this using old version java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I sorted.bam -o sorted.intervals Now there is not any GenomeAnalysisTK.jar or RealignerTargetCreator and I am using a newer vers ...
genomics written 6 days ago by Learner 130

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Popular Question 7 months ago, created a question with more than 1,000 views. For how to convert SwissProt or UniProt gene names to standard ID
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