User: manuel.belmadani

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Posts by manuel.belmadani

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Answer: A: Clipping reads within BAM files?
... Do you have the FASTQ files? I'm asking because if the sequence do need clipping, then your BAM file possibly has reads that were unaligned or misaligned because clipping wasn't done. So why not clip the FASTQs and re-align? If you don't, but still want to try, you could could use a tool to extrac ...
written 1 day ago by manuel.belmadani1.1k
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Answer: A: Pheatmap row annotation multiple categories
... There's two ways I can see you do this. An easy way is to add just a "both" value (as I see now Kevin suggested in the comment.). In this case it makes sense since there's only two choices. ![Using a category for cases that are "both"][1] Or if you really want to (or will have cases where "both" d ...
written 5 days ago by manuel.belmadani1.1k
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Answer: A: unsuccessful RnBeads installation
... What did you try, and what error message did you get? The standard bioconductor installation worked for me (`R version 3.5.0`). if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RnBeads") ...
written 3 months ago by manuel.belmadani1.1k
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Comment: C: SAM file generation problem
... Can show us the file sizes for your original and trimmed data, as well as your genome? One thing I notice is that in your cutadapt command, the quality filter (`-q 30`) is **after** the input files whereas in the documentation it's typically before. If your trimmed files are suspiciously small I w ...
written 3 months ago by manuel.belmadani1.1k
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Comment: C: SAM file generation problem
... In the future when you paste code examples, highlight your code and click the "101 010" button to make it a code block, makes it easier to read. ![Formatting options][1] [1]: https://i.imgur.com/YKBXxos.png ...
written 3 months ago by manuel.belmadani1.1k
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Answer: A: SAM file generation problem
... Change `--dta -cufflinks` to `--dta-cufflinks`. ...
written 3 months ago by manuel.belmadani1.1k
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Answer: A: Genomic screen: Benjamini-Hochberg procedure
... > If I assume these seven sgRNA's would be enriched, based on previews published studies, is it correct to rank the p-value of the seven sgRNA's higher in my BH analysis for corrected p-value? I don't think so. I wouldn't incorporate information from "previous studies" without doing a proper met ...
written 3 months ago by manuel.belmadani1.1k
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Comment: C: how to grep list of words from a file to another file
... If I understand correctly, you would be grepping `>NODE_1_length_232048_cov_20.4417`, not `NODE_1_length_232048_cov_20.4417`, so that wouldn't work. I'm assuming the sequence is also not of interest since you only care about the header? If that's the case, preprocess your fasta file into expres ...
written 3 months ago by manuel.belmadani1.1k
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Comment: C: Find motif in reads and delete everything before / extract everything after
... When you linearize, you could prefix the input to the sed command with a grep for `atgacccg`, i.e. grep "atgacccg" my_linearized.fasta | sed -e 's|.*atgacccg\(.\{3\}\).*|\1|g' my.fasta > only_matching_atgacccg.fasta That way only sequences matching `atgacccg` are retained and processed b ...
written 3 months ago by manuel.belmadani1.1k
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Comment: C: how to grep list of words from a file to another file
... How many expressions are you searching, and how many lines in your gff? It looks like you're trying to match a FASTA file to a GFF file, is that correct? You example seemed different. I just tested with the exact input your provided and it works here. If your inputs are different than what was in ...
written 3 months ago by manuel.belmadani1.1k

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