User: jordi.planells

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Posts by jordi.planells

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Comment: C: .sra to bam conversion results in a "< myfile > does not have BAM or CRAM format
... Thanks for your help! this worked smoothly. ...
written 11 weeks ago by jordi.planells80
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Comment: C: .sra to bam conversion results in a "< myfile > does not have BAM or CRAM format
... 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.planells80
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Comment: A: .sra to bam conversion results in a "< myfile > does not have BAM or CRAM format
... 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.planells80
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Comment: C: .sra to bam conversion results in a "< myfile > does not have BAM or CRAM format
... 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.planells80
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Comment: C: .sra to bam conversion results in a "< myfile > does not have BAM or CRAM format
... The accession number I am looking at is SRP060510, which consists of 4 samples: SRR2089860, SRR2089861, SRR2089862, SRR2089863 ...
written 11 weeks ago by jordi.planells80
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.sra to bam conversion results in a "< myfile > does not have BAM or CRAM format error"
... 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 ...
sra-toolkit samtools deeptools written 12 weeks ago by jordi.planells80 • updated 11 weeks ago by genomax70k
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Answer: A: How to extract fasta sequence of lncRNA from whole ncRNA fasta of ucsc ftp downl
... 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.planells80
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geom_bar plot with several variables
... 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 ...
R ggplot2 written 6 months ago by jordi.planells80 • updated 7 weeks ago by gpushpaganesan0
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Comment: C: Using forloop to add headers to multiple files
... Thank you too, arup! ...
written 7 months ago by jordi.planells80
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Comment: C: Using forloop to add headers to multiple files
... Thank you a lot!! It is really appreciated ...
written 7 months ago by jordi.planells80

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Popular Question 3 months ago, created a question with more than 1,000 views. For geom_bar plot with several variables

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