User: jordi.planells
jordi.planells • 80
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Posts by jordi.planells
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... Thanks for your help! this worked smoothly.
...
written 11 weeks ago by
jordi.planells • 80
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... I have posted more commands today because I have performed further checks this morning as I was not able to get the .bam (following the suggestions from other users). Thank you for the tutorial, I will give it a shot and try to get the fastq files how is explained there. ...
written 11 weeks ago by
jordi.planells • 80
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... I have performed other operations:
`vdb-validate` -> everything seems to be fine
`fastq-dump` -> resulting in the following error "Error: reads file does not look like a FASTQ file" ...
written 11 weeks ago by
jordi.planells • 80
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... I have checked. I get the following message: SRR2089860.bam had no targets in header (for all 4 of them) ...
written 11 weeks ago by
jordi.planells • 80
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... The accession number I am looking at is SRP060510, which consists of 4 samples: SRR2089860, SRR2089861, SRR2089862, SRR2089863 ...
written 11 weeks ago by
jordi.planells • 80
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... Hi all! I am having problems and I hope I can get some help from you.
I will explain my situation: I'm trying to perform a PCA analysis to see how different several bam files are. I'm using the next pipeline:
1.
Getting the accession files. I am using the R library "SRAdb", so I am getting 4 fil ...
written 12 weeks ago by
jordi.planells • 80
• updated
11 weeks ago by
genomax ♦ 70k
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... You can always try with `bedtools getfasta -fi -fo -bed `
1 observation! Be careful if you are using macOS with the carriage return (see info [here][1] if needed), as your fasta will contain only the first lane of your bed annotation.
Cheers, and I hope it's useful
[1]: https://stackoverflo ...
written 4 months ago by
jordi.planells • 80
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... Hi all, I need your help. I am struggling on getting a bar plot with ggplot2 package.
Imagine I have 3 different variables (which would be my y values in aes) that I want to plot for each of my samples (x aes):
str(df)
'data.frame': 4 obs. of 4 variables:
$ samples: Factor w/ 4 ...
written 6 months ago by
jordi.planells • 80
• updated
7 weeks ago by
gpushpaganesan • 0
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... Thank you too, arup! ...
written 7 months ago by
jordi.planells • 80
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... Thank you a lot!! It is really appreciated ...
written 7 months ago by
jordi.planells • 80
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3 months ago,
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For geom_bar plot with several variables
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