User: haro

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haro200
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Posts by haro

<prev • 70 results • page 1 of 7 • next >
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Comment: C: Principal Component Analysis: How many most variant genes should I take?
... If you sum PC1 and PC2, ntop =500 obtain 69, the other are below. I would take 500, because it explains globally better your results ...
written 4 weeks ago by haro200
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Comment: C: count of reads having multiple references
... Yes wc is definitively what I need to count Here is the error (certainly due to a lack of computing power, because it works for some of my files and I couldn't detect any corrupted files): auto.sh : ligne 7 : 4800 Relais brisé (pipe) samtools view file55-sorted.bam 4801 Processus ...
written 5 weeks ago by haro200
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count of reads having multiple references
... Hi all, I have done an alignment using bwa on numerous references and I would like to retrieve a count of the reads matching more than one references and know witch references are involved. This question is related to this post : [https://www.biostars.org/p/274429/][1], but here I don't need to ge ...
read alignment multiple references written 5 weeks ago by haro200
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Answer: A: Any alternative (free, open source tool) for Geneious software for phylogenetic
... Have a look at [Jalview][1] [1]: http://www.jalview.org/ ...
written 6 weeks ago by haro200
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Comment: C: How to highlight multiple references mapped reads?
... Hi Pierre, Thank you for your answer, that's what I've tried but I wanted to be sure that I miss anything I tried this: samtools view -F 4 file.bam | cut -f1,3 | sort | uniq | cut -f1 | sort | uniq -d > names.txt samtools view file.bam | grep -f names.txt > sequences.sam cat s ...
written 7 weeks ago by haro200
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Comment: C: How to highlight multiple references mapped reads?
... Thanks a lot for your answer! What about single reads dataset? ...
written 8 weeks ago by haro200
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Comment: C: How to highlight multiple references mapped reads?
... I just meant to work with them after. Sorry if my question is not clear : I'm trying to get two different things: - make a file containing reads (matching with 2 references or more) and with which references associated - a count that tell me that x reads match with references 'a' and 'b', y reads w ...
written 8 weeks ago by haro200
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How to highlight multiple references mapped reads?
... Hi all, A very basic question but I can't solve it easily. After a raw-read mapping against a list of references, how to make a list of reads that match with more than one reference (and which ones) to highlight them? Thank you very much! ...
alignment written 8 weeks ago by haro200 • updated 8 weeks ago by Pierre Lindenbaum101k
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Comment: C: Good pratice for clinical NGS data pipelines
... Hi Chen, Thank you for your answer, your pipeline is cool, very clear and well documented but except for read filtering I don't see any controls, graphs or reports to validate quality of the data and also analysis process ...
written 8 weeks ago by haro200
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Good pratice for clinical NGS data pipelines
... Hello everyone! I have a very general question. Does anybody have advices, guidelines, papers, softwares about good practice for clinical NGS data pipelines? My aim is to set up a quality process for my lab using a home made build pipeline or something already existing. What I have in mind (but d ...
tools good practices clinical ngs written 8 weeks ago by haro200 • updated 8 weeks ago by chen1.1k

Latest awards to haro

Scholar 6 weeks ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Scholar 3 months ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Supporter 7 months ago, voted at least 25 times.

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