User: Rad

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Rad780
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780
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Canada
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1 year, 4 months ago
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Posts by Rad

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Somatic mutations database with corresponding bam files
... Ok sorry for that, wasn't my intention, not a frequent user ...
written 16 months ago by Rad780
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Comment: C: Somatic mutations database with corresponding bam files
... what ? I didn't add an answer so that the post reappear on the main page, I just wanted to refresh the question for some help what makes you think that ? ...
written 16 months ago by Rad780
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Comment: A: Somatic mutations database with corresponding bam files
... any input on this question is more than welcome ...
written 16 months ago by Rad780
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Somatic mutations database with corresponding bam files
... Hello there I was wondering if someone could point to a resource where we can download validated somatic mutations as well as their corresponding alignments (bam files) I found several repositories and databases (COSMIC etc ..) but as far as I know they don't offer location where to get the origin ...
somatic bam mutation variant written 16 months ago by Rad780 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: Bwa And Bwa Mem Produce Different Alignments
... Yes, we had an experiment in the lab that was not suppose to give a bullet proof alignment, bwa-mem failed in the sense that it was trying to align the sequences anyway, which is not supposed to happen, which means the result does not make sense biologically. I ended up preferring bowtie2 on bwa for ...
written 2.9 years ago by Rad780
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Answer: A: When exit code is not enough
... Thank you all for your contributions. To all those who will be interested in this kind of problems, the overall message that should be retained from this discussion is : when there is a problem in the source, it should be treated in the source, whatever wrapper, codes, tricks that you may end up do ...
written 3.0 years ago by Rad780
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Comment: C: When exit code is not enough
... I agree with you Istvan, this is basically what we have to do on a daily basis (working around the problems) but these are basics of soft eng (being able to distinguish stderr / stdout / managing exit codes etc ..), and for reproducibility sake one should be able to just look at the log to get sense ...
written 3.0 years ago by Rad780
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Comment: C: When exit code is not enough
... That's possible in case we do know the expected output file, sometimes it is not possible to predict, I mean if the branch of that pipeline is itself subject to a condition ...
written 3.0 years ago by Rad780
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Answer: A: When exit code is not enough
... Strangely samtools view returns the right status in case of a problem, an example is posted @ CodersCrowd ...
written 3.0 years ago by Rad780
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When exit code is not enough
... There is a lot of tools out there, very useful for command line usage, and very widely used in Bioinformatics, which rapidly turns out to be annoying (may be, sometimes) if we are writing a pipeline that cares about I/O connection and each tasks' exit status. I am writing a pipeline using samtools ...
python exit code samtools written 3.0 years ago by Rad780

Latest awards to Rad

Great Question 2.3 years ago, created a question with more than 5,000 views. For FastQ quality check : what can we correct ?
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For FastQ quality check : what can we correct ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Coderscrowd - Bioinformatics Crowdcoding Platform To Be Launched On November
Popular Question 2.3 years ago, created a question with more than 1,000 views. For When exit code is not enough
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Variant Callers for deep sequencing
Popular Question 2.3 years ago, created a question with more than 1,000 views. For FastQ quality check : what can we correct ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bwa And Bwa Mem Produce Different Alignments
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bwa And Bwa Mem Produce Different Alignments
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bwa And Bwa Mem Produce Different Alignments
Scholar 3.0 years ago, created an answer that has been accepted. For A: When exit code is not enough
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Create A Bioinformatics Pipeline Using Spotify !
Appreciated 3.3 years ago, created a post with more than 5 votes. For FastQ quality check : what can we correct ?
Appreciated 3.4 years ago, created a post with more than 5 votes. For Coderscrowd - Bioinformatics Crowdcoding Platform To Be Launched On November
Student 3.4 years ago, asked a question with at least 3 up-votes. For Variant Callers for deep sequencing
Appreciated 3.5 years ago, created a post with more than 5 votes. For Coderscrowd - Bioinformatics Crowdcoding Platform To Be Launched On November
Student 3.5 years ago, asked a question with at least 3 up-votes. For Variant Callers for deep sequencing
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Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: #Bioinformatics Crowdcoding
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